Human evolution (Part 2): My response to the arm chair experts and their criticism

Byrd - thank you as always. Sweet voice of educated reason, unencumbered by onerous ego.

tauristercus - I think your basic observation is intriguing and if developed with respect to larger implications, could be fruitful. However - focusing on the mechanics of mutation is likely inappropriate. The mechanics of "genetics" cannot be fully apprehended or elucidated at this point - if you continue in this vein, you'll trip, the bear trap will close and the investigative potentials inherent in your observation will be lost.

My take home point from you is this:

Evolution started 3.1 Billion years ago, and has continued unabated ever since.

…However it happened, it did happen. Ignoring the mechanics as beside the main point, where can you go with this simple observation?

tgidkp
…mutation is NOT a totally random process. it is a result of predictable mechanical molecular processes gone awry. the cellular mechanics of replication and recombination were the very first processes to have evolved. thus, there is a bit of structure involved. it is this marriage between pre-determined rules and randomness that accounts for species variability.

tgidkp - tauristercus is looking at the dawn of life - from the first cell - before organisms, patterns, "rules" and processes emerged.

How can there have been "predictable mechanical molecular processes" when no processes were yet established?

….I suspect you may be trying to turn this into a debate: 12 Monkeys pecking randomly versus Intelligent Design. Not on point, not relevant, not fruitful. imho If my suspicions are off the mark, I apologize.

Now, despite my admonition to tauristercus NOT to focus on mechanics, that's precisely what I intend to do.

…Here's a monkey wrench I quite enjoy, and I'd like you ALL to consider the implications, if you would please.

It's now known that:
1. Individual bacteria (not just the population) can adapt to a changing environment at the DNA level, and THEN
2. Purposefully transfer that adaptive genetic information horizontally to their neighbors. In other words, the genetic information is NOT "inherited" or passed on "genetically" - it's transferred like an 'infection.'

Just noticed that mattison0922 posted on this VERY intriguing information back in May of 2009, when the studies got renewed attention.

mattison0922

This article details the molecular mechanism behind the transfer of resistance genes between bacteria. …New rearrangements are triggered by taking an antibiotics, and those bacteria that have 'correctly' rearranged their genes, creating a new resistance cassette, will be able to survive and pass on this resistance not only vertically, but also horizontally - to their peers; bacteria can pass resistance genes to their neighbors in a deliberate manner.

This is extremely significant; the classic Darwinian story describes the organism as entirely a slave to the environment, unable to respond or adapt at the individuallevel. Only a lucky few - those that are resistant by chance - survive the selective pressure of antibiotic use, and are able to pass on their genes.

Or as you've been more simply taught: Survival of the fittest.

This new research clearly indicates that this is not necessarily the case, and in fact, contrary to what I've been taught more-or-less through my entire history in science - individual organisms - not just populations are able to not only react to, but also to adapt to the environment.

At least individual microorganisms are able to do this.

It cannot be stressed enough how significant of a break this is from the classic story of antibiotic resistance via Darwinian evolution. The idea that the individual and not just the population of organisms can adapt to a changing environment at the DNA level is literally scientific heresy.

This is of course more evidence, another huge piece of evidence suggesting that The Theory of Evolution with respect Darwin's ideas is at least not as well understood as was once believed, and at most completely, utterly, and totally false.

Also see: mattison0922
ORIGINAL SOURCES:
Molecular Mechanisms of Antibacterial Multidrug Resistance
The SOS Response Controls Integron Recombination

For the sake of argument, let's assume that ALL species have this capacity to share genetic information horizontally - to "infect" other members of their species with genetic information. Where does that lead?

1. The first thing that comes to my mind is delightfully amusing. Visualize a group of elite rulers, exceedingly proud of their "superior" bloodlines and their thousand-year pedigrees - being fed, served and dressed by "genetically inferior" peasants.

…Not only are the "elite" sharing their "superior" genetic information with peasants, but their own "superior bloodline" is being contaminated by genetic information passed horizontally from their "inferior" peasant servants.

…This is, of course, absolute heresy. Unthinkable. And imho, not just most probable, but really, really funny.

2. "Eugenics" didn't die after WW2, it went underground in our hallowed halls of learning, was renamed "Genetics" and went on to "inform" virtually every discipline on the curriculum. Most geneticists, sociologists, doctors, medical researchers, policy analysts and lawmakers have been trained, educated and programmed to accept the premise that some bloodlines are "genetically superior" and others "genetically inferior." That only the "fittest" survive. At best, they offer lip-service to the notion that environment may be a factor in development.

Right or Left - Policies for birth control, population reduction and control are all premised on the notion that "inferior human stock" needs to be controlled, if not eradicated. Economic and other policies that readily accommodate the notion of 'collateral damage' are informed, justified and rationalized by Eugenics postulates.

BUT…

…IF any individual can develop successful adaptive traits,
THEN
…virtually any individual -rich, poor, healthy, sick, educated, uneducated- may have the genes required to ensure the human species survival in our planet's radically changed environment,
AND
…any interventionist eugenics policy risks depriving the entire human species of genetic information essential to ensuring the human species' survival - not just that individual's potential progeny.

Further,

…IF an individual can develop, then pass along adaptive genetic information as infection,
THEN
…no interventionist eugenics policies make any sense. At all.


This 'bank' of research shows that genetic information can be transferred horizontally not just between members of the same species, but across species barriers too. Other research shows that some genetic information crosses not just species barriers, but kingdom barriers as well.

So what if…

What if ALL living organisms exchange and share genetic information essential to survival? What if every distinct genome isn't really that distinct? What might that imply?

Originally posted by soficrow
...How can there have been "predictable mechanical molecular processes" when no processes were yet established?...

bootstrapping is a mind-bender. how did the first pro-active molecular symbol appear? at the end of my molecular biology textbook there is a whole chapter about it which is full of all types of laughable mythical creatures. it literally reads like a fantasy novel. if this were what the OP were speculating about, and ONLY this, then i am certain that no one would have had a problem with that.

at the end of my last post i put that image of cellular automata to address this exact issue in the way that makes the most sense to me. all that is needed to get off the ground are a couple of simple rules. conformational rules, if you like, similar to the prions you had been talking about before. simple RNA sequences that would be capable of enforcing a reliable behavior pattern in their neighboring molecules. from there, it reads just like the cellular automata image. novel structures crop up unpredictably and are incorporated into the basic rules set. and on and on and on....

what is most interesting about the "novel structures that crop up unpredictably" is that they seem to have been there all along, inherent within the initial conditions yet invisible until expressed. this implies a certain backwards causality which is one of my favorite topics. for further reading, see rupert sheldrake's amazing theory of formative causation.

this is very similar to what the OP has been trying to express: a type of turbo-charge on evolutionary process. but, shhhhhh......dont tell him.

...bacteria can pass resistance genes to their neighbors in a deliberate manner...

deliberate?! deliberate?! whoa.....slow down there. you are being overly generous about this. F plasmid inheritance is best described as a fortunate series of accidents.

ACCIDENT #1: a suitable antibiotic resistance would have to emerge in a "female" cell which would then have to become the recipient of a "male" F plasmid carrier.
ACCIDENT #2: the F plasmid must insert itself into the host chromosome at a position in which the 'F insertion sequence' directly flanks the novel resistance gene.
ACCIDENT #3: the novel resistance gene can now be passed on to other "females" ONLY. this means that cells currently carrying an F plasmid (males) are doomed.

in order to obtain multiple resistance factors, this series of accidents must be repeated. it almost never happens, but when it does, it produces quite a nasty bug indeed. but to call this process deliberate is misleading at best.

... let's assume that ALL species have this capacity to share genetic information horizontally - to "infect" other members of their species with genetic information...

okay. ill buy that it is plausible. horizontal transfer in complex organisms would probably be under even worse odds than the "accidents" i described above. but in the end, it is purely a matter of sequence homology. if the foreign sequence is similar enough to the host sequence and at the right place at the right time, then recombination will probably occur.

there, you see: i CAN be open-minded.

reply to post by tgidkp


S& for being funny and cool too.

RE; "deliberate." mattison said that, not me. ...but I have no trouble assigning anthropomorphic awareness to microbes. Really, I don't. Although I would probably insert a qualifier and specify a kind of "hive" consciousness whilst wildly speculating on the necessity of same for the creation of biofilm communities.

... let's assume that ALL species have this capacity to share genetic information horizontally - to "infect" other members of their species with genetic information...

okay. ill buy that it is plausible. horizontal transfer in complex organisms would probably be under even worse odds than the "accidents" i described above.

How 'bout if a microbe is available to act as an "intermediary"?

...but in the end, it is purely a matter of sequence homology. if the foreign sequence is similar enough to the host sequence and at the right place at the right time, then recombination will probably occur.

Hmm. A lot of evidence suggests that epigenetics is FAR more important that genetics.

there, you see: i CAN be open-minded.

Uh huh. You're good. Now, s-t-r-e-t-c-h.

Think of swine and bird flu (for example), and visualize them as vehicles carrying plasmids and prions between species, and from individual to individual.

Does that work for you? Conceptually?



Ed. to add:

Called away, will leave above alone/unedited. But, want to recommend a book - Byrd, tgidkp - maybe tauristercus.

Biological Emergences: Evolution by Natural Experiment (Vienna Series in Theoretical Biology)
Author: Robert G. B. Reid

Natural selection is commonly interpreted as the fundamental mechanism of evolution. Questions about how selection theory can claim to be the all-sufficient explanation of evolution often go unanswered by today’s neo-Darwinists, perhaps for fear that any criticism of the evolutionary paradigm will encourage creationists and proponents of intelligent design.

In Biological Emergences, Robert Reid argues that natural selection is not the cause of evolution. He writes that the causes of variations, which he refers to as natural experiments, are independent of natural selection; indeed, he suggests, natural selection may get in the way of evolution. Reid proposes an alternative theory to explain how emergent novelties are generated and under what conditions they can overcome the resistance of natural selection. He suggests that what causes innovative variation causes evolution, and that these phenomena are environmental as well as organismal.

After an extended critique of selectionism, Reid constructs an emergence theory of evolution, first examining the evidence in three causal arenas of emergent evolution: symbiosis/association, evolutionary physiology/behavior, and developmental evolution. Based on this evidence of causation, he proposes some working hypotheses, examining mechanisms and processes common to all three arenas, and arrives at a theoretical framework that accounts for generative mechanisms and emergent qualities. Without selectionism, Reid argues, evolutionary innovation can more easily be integrated into a general thesis. Finally, Reid proposes a biological synthesis of rapid emergent evolutionary phases and the prolonged, dynamically stable, non-evolutionary phases imposed by natural selection.

...Confess I haven't read it - but comes highly recommended by a friend interested in complexity and chaos theory - Reid approaches bio-evolution from the perspective of emergent self-organization.

Originally posted by soficrow
Think of swine and bird flu (for example), and visualize them as vehicles carrying plasmids and prions between species, and from individual to individual.

Viroids carrying plasmids? I don't think so. Prions are by definition proteins. No coating. No envelope. Nothing. They move about by chance, but as far as I know never cause anything beneficial as they're just misfolded proteins than proteases can't act upon, but which change conformation of related proteins and thus you get aggregates and eventual destruction.

Retroviruses could in principle transfer maybe even small genes from one organism to another, but there you run to the problem, that their entry to cell is receptor specific, thus they don't do the cross species thing..

reply to post by rhinoceros


Much evidence suggests that prions abound - and at least some are beneficial.

Leaving that aside for the moment, here's an article from 2002, stipulating that the phenomenon of horizontal gene transfer is NOT 'old' but in fact, results from genetic engineering:

Recent Evidence Confirms Risks of Horizontal Gene Transfer

ISIS Contribution to ACNFP/Food Standards Agency Open Meeting 13 November 2002

Horizontal gene transfer is one of the most serious, if not the most serious hazard of transgenic technology. I have been drawing our regulators’ attention to it at least since 1996 [1], when there was already sufficient evidence to suggest that transgenic DNA in GM crops and products can spread by being taken up directly by viruses and bacteria as well as plant and animals cells.

The oft-repeated refrain that "transgenic DNA is just like ordinary DNA" is false. Transgenic DNA is in many respects optimised for horizontal gene transfer. It is designed to cross species barriers and to jump into genomes, and it has homologies to the DNA of many species and their genetic parasites (plasmids, transposons and viruses), thereby enhancing recombination with all of them [2]. Transgenic constructs contain new combinations of genes that have never existed, and they also amplify gene products that have never been part of our food chain [3].

The health risks of horizontal gene transfer include:

Antibiotic resistance genes spreading to pathogenic bacteria.
Disease-associated genes spreading and recombining to create new viruses and bacteria that cause diseases.
Transgenic DNA inserting into human cells, triggering cancer.

Whatcha think?

Originally posted by soficrow
Much evidence suggests that prions abound - and at least some are beneficial.

Leaving that aside for the moment, here's an article from 2002, stipulating that the phenomenon of horizontal gene transfer is NOT 'old' but in fact, results from genetic engineering:

What evidence suggests that prions are beneficial? They destroy brains. I've never heard of anything good. What goes for your citation. It doesn't claim what you say. Horizontal gene transfer is very old phenomenon. It's likely that every single prokaryote gene has been horizontally transferred during prokaryote evolution (via conjugation, transformation & transduction). Your citing speaks of transduction.

reply to post by rhinoceros

rhinoceros
What evidence suggests that prions are beneficial? … I've never heard of anything good.

Here's a quick overview:

* The beneficial side of prions

* Redefining what it means to be a prion:

“We think that the fact that prions are sometimes beneficial and sometimes detrimental for the yeast is at the heart of their biology – that they present a sort of bet-hedging strategy, where in some circumstances it’s good to be in the prion state and in some cases it’s not,” says Whitehead Member and Howard Hughes Medical Institute Investigator Susan Lindquist.

* Beneficial Role of Prions in Brain Function:

...prions possess a hazardous status. Regardless of this depressing nature, a recent research describes certain essential positive responsibilities of prions in brain function. A persistent problem in the study of memory is how molecules in the brain can “remember” a memory for years, even a lifetime. How it is that our brain’s cells can permanently store information that we learn?

Researchers at the Stowers Institute of Medical Research reveals that prion like protein may participate in persistence of memory in eukaryotes. The research led by Kausik Si of Stowers Institute for Medical Research and Nobel laureate Eric Kandel suggest that prions may be the best solution to the problem. Prions marked the ability to assume two distinct conformational states – one is dominant and self perpetuating. Once a protein switches to prion state it has the ability to convert other non prion proteins to that state. Thus once engaged the prion state, it continues to be self-renewing and stable.

The study concludes that memory traces may depend on a fairly unique mechanism involving a prion-like protein known as CPEB. CPEB (cytoplasmic polyadenylation element binding protein) was involved in memory formation in the sea slug Aplysia.

* Large Number Of New Prions Discovered: Scientists Redefining What It Means To Be A Prion

Special proteins known as prions, which are perhaps best known as the agents of mad cow and other neurodegenerative diseases, can also serve as an important source of beneficial variation in nature. Whitehead Institute researchers have quintupled the number of identifiable prion proteins in yeast and have further clarified the role prions play in the inheritance of both beneficial and detrimental traits.

…Prions in cells are known to switch back and forth between a clumping, infectious stage and a non-infectious stage. When yeast is stressed, this switching occurs at a higher rate, which may give the yeast a better chance to adapt to challenging conditions.

* An interesting blog on the topic: The beneficial prion, evolution and the origin of life

Are there any beneficial prions? It is thinkable, and in fact there is an example of it. In yeast, a prion has been identified which in certain circumstances is beneficial, see for example Prions act as stepping stones in evolution. The remarkable thing is that the effect can be passed on to the offspring.

…when it misfolds into a prion conformation, Sup35 gets sloppy, and the cell reads beyond the stop codons, translating genetic information that previously had been dormant. As a result, the cell's phenotype changes.

And here's where evolution comes in.

On those rare occasions when, due to a particular environment, the altered properties of the cell provide it with a survival advantage, the cell passes that trait on to its progeny. But when the daughter cells are mated and genetic reassortment takes place, they can subsequently pass along this same trait without the prion. That is, the trait becomes fixed in the cell's lineage and no longer depends on the prion state. "We don't know yet exactly how the daughter cells do this, but they do it quickly, often after a single mating," said Lindquist.

The prion thus appears to function as an evolutionary stepping stone, affording the population of cells a chance to survive in a new environment where they need a different phenotype until they can acquire the genetic changes that produce the same effect.

These new traits are genetically complex. When Sup35 misfolds into a prion form, it affects a number of genes in one fell swoop.

"This prion has a capacity to hide and release genetic information throughout the entire genome that can contribute to new traits in a complex way," explained Lindquist.

RE: Your questions about prions, plasmids, viruses.

Prions hitchhike on and/or infect microbes - and "ectoparasites" like flies also 'harbor' prions.

Animal prion infections, such as scrapie (sheep) and "mad cow disease" (cattle), have shown a pattern of horizontal transmission in farm conditions and several ectoparasites have been shown to harbor prion rods in laboratory experiments. Fly larvae and mites were exposed to brain-infected material and were readily able to transmit scrapie to hamsters. New lines of evidence have confirmed that adult flies are also able to express prion proteins. ...Several cell types found on the human skin, including keratinocytes, fibroblasts and lymphocytes, are susceptible to the abnormal infective isoform of the prion protein, which transforms the skin to produce a potential target for prion infection.

Int J Dermatol. 2003 Jun;42(6):425-9. Could ectoparasites act as vectors for prion diseases? Lupi O. Center for Vaccine Development, University of Texas Medical Branch at Galveston, Galveston, TX, USA. PMID: 12786866

This 1986 paper describes how "proteinaceous capsids" (prions) use viruses as vehicles of transmission...
* Viral influences on aflatoxin formation by Aspergillus flavus. Appl Microbiol Biotechnol 24:248-252. Schmidt FR, Lemke PA, Esser K (1986)

Epidemiological observations indicate that a microbial vector is responsible for the transmission of natural prion disease in sheep and goats … ...It is proposed that many microbial proteins may be capable of replicating themselves in mammalian cells eliciting and sustaining thereby degenerative and/or autoimmune reactions subsequent to infections with microorganisms.

* Med Hypotheses. 1999 Aug;53(2):91-102. Is the pathogen of prion disease a microbial protein? Fuzi M. Budapest Institute of National Public Health and Medical Officer Service, Hungary. PMID: 10532698

* Dangerous liaisons between a microbe and the prion protein. J Exp Med. 2003 Jul 7;198(1):1-4. Aguzzi A, Hardt WD. PMID: 12847133

Prions are mainly found in the brain, spinal cord and immune system. …in a series of studies, Aguzzi's group has shown that prions can be present in other organs as well, provided that these organs are inflamed. …Earlier this year, his group found prions in inflamed pancreases, livers and kidneys. A study last month showed that the urine produced by inflamed kidneys in mice also contains prions.
…And it prompted Aguzzi to look at mammary glands to see if they could carry prions too.

The mammary-gland infections were caused by a virus called Maedi Visna. Aguzzi says that if this prion-virus combination is common, it may be a clue to how to fight the transmission of scrapie. "Maybe to eradicate scrapie you have to eradicate the virus first," Aguzzi says.

Source: Nature

ALSO OF INTEREST

We discovered two prions (infectious proteins) in S. cerevisiae, called [URE3] and [PSI]. In doing so, we proved that a protein can be a gene.

Source: The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), part of the National Institutes of Health (NIH) and the U.S. Department of Health and Human Services.

rhinoceros
What goes for your citation. It doesn't claim what you say. Horizontal gene transfer is very old phenomenon. It's likely that every single prokaryote gene has been horizontally transferred during prokaryote evolution (via conjugation, transformation & transduction). Your citing speaks of transduction.

You're right - my birds were screaming at me and my dog was agitating for his walk - wrote too fast, buggered my phrasing.

Dr. Ho was focusing on the fact that transgenic DNA is optimised for horizontal gene transfer:

…transgenic DNA in GM crops and products can spread by being taken up directly by viruses and bacteria as well as plant and animals cells.

Transgenic DNA is in many respects optimised for horizontal gene transfer. It is designed to cross species barriers and to jump into genomes, and it has homologies to the DNA of many species and their genetic parasites (plasmids, transposons and viruses), thereby enhancing recombination with all of them [2]. Transgenic constructs contain new combinations of genes that have never existed, and they also amplify gene products that have never been part of our food chain [3].

Also see: See Ho MW. Horizontal Gene Transfer. The Hidden Hazards of Genetic Engineering, TWN Biotechnology Series, Third World Network, 2001 (available fom the ISIS online store); also Ho MW. Horizontal gene transfer and genetic engineering, SCOPES website, AAAS, 2000.

Just to confirm, transduction is a type or mechanism of Horizontal Gene Transfer:

Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g., its parent or a species from which it has evolved.

Most thinking in genetics has focused upon vertical transfer, but there is a growing awareness that horizontal gene transfer is a highly significant phenomenon and amongst single-celled organisms perhaps the dominant form of genetic transfer. Artificial horizontal gene transfer is a form of genetic engineering. ...

Mechanism

There are several mechanisms for horizontal gene transfer:

* Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA). …
* Transduction, the process in which bacterial DNA is moved from one bacterium to another by a bacterial virus (a bacteriophage, or phage).
* Bacterial conjugation, a process in which a bacterial cell transfers genetic material to another cell by cell-to-cell contact.
* Gene transfer agents, viruslike elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales.[10]

rhinoceros
Retroviruses could in principle transfer maybe even small genes from one organism to another, but there you run to the problem, that their entry to cell is receptor specific, thus they don't do the cross species thing..

Seems this is where prions come in - they are "keys" that "unlock the doors" by providing the conformation required to ensure cell access.

reply to post by soficrow


i actually did a lot of thinking about how to answer you. there are plenty of known mechanisms in genomics that would make what you suggest possible.

i recently came across an idea that would make horizontal transfer even more plausible. i started a new thread about it HERE.