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« Do You Want to Avoid the Bottleneck? | Main | Remember »

November 28, 2013

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Reverse Engineer

" The origin of life problem is far from solved in detail, but the broad outlines of what compounds needed to be synthesized in advance of protocell organization is understood well enough to be confident in saying that the pre-life conditions could create a milieu in which further auto-organization of those component parts led to protocells with heritable, stable genetic material and the triggering of neo-Darwinian evolutionary mechanism."-GM

Where do you get this confidence George?

In the lab you can set up the proto-life conditions you THINK might have existed in the "primordial ocean", and even go so far as to drop in all the molecules necessary for life as well under the assumption that they were produced somehow in sufficient concentration to all self-organize.

Even if you do all that AND provide an energy source and gradient, you can't get self replicating organisms out of it.

So why are you so confident that spontaneous generation fo life is possible simply from thermodynamic principles? There is no real evidence of any sort for this.

RE
http://doomsteaddiner.net

D. Aaron Fiore

"The reduction in the power available to human culture may mean an end to the kind of culture we have become used to. But it does not mean an end to human evolution. As long as there is sunlight some humans can and will survive, even thrive..."

I hope you are correct. Apologies if this has been hashed over previously, but what about concerns, voiced in some quarters, concerning the several hundred nuclear power plants distributed around our planet? While said "survivors" huddle 'round their campfires, what will prevent unmonitored nuclear plants from going critical and, IMHO, potentially reducing post-bottleneck human numbers to .... zero?

Paul H.

But, if the environment were to stay the same, evolution would stop (I am discounting sexual and cultural selection as the main drivers of human evolution). Evolution only provides a species fit enough to thrive in a particular environment at a particular time.
The environment, obviously, does not stop changing, therefore, evolution does not stop altering species to fit those changes.
That is the extent of evolution though. There is no plan to produce a super-species of humans.
If the coming new environment precludes this new species then it will not even evolve, let alone thrive.

Ulises_Jofre

Is there evolution if there is no time? How the physical new paradigms affect the conceptual structure of biological evolution? Psychologically, is there change if there isn't verbal thought? If you want, take a look of this book, you will perhaps get some original ideas to go on questioning, just a different aproach. A sample in: http://goo.gl/IUlSMu

Tom

George: great read! I have come to the conclusion that sapience is a made-up quality, an imaginative myth, a quality it would be nice if we had, but don't in any appreciable or meaningful number to make any difference to our coming extinction by our own hand. Thanks for supplying the scholarly working papers from the last thread.

We're a creative species - oh we can invent and find ways around limiting factors from the environment - but we aren't wise enough to see them for what they are, protecting mechanisms.

We simply refuse to accept the idea that we're nothing special and have our time on the earth like all other species and then we're "shown the door." All the so-called progress (especially the complexity) we've attained over our past millennia have led to the over-shoot, biosphere degradation and habitat destruction that will be our un-doing in the not-too-distant future, according to prevailing scientific evidence (like all the self-reinforcing feedback loops that will continue to make the planet less able to sustain our species in the coming years - on top of all the natural forces like solar influences, volcanic activity and the social collapse of human civilization).

Thanks for taking the time to consider my point, even though you disagree. I appreciate your being grounded enough to allow dissent, and, like all the other visitors here, enjoy reading your thoughts - even if they seem like science fiction at times.

George Mobus

@RE,

Your description of what we "can do" sounds so 1960s! A lot has been going on since Miller-Urey, et al. Some of the references I gave have some updates. But I will add two more for you to look at and see the evidence for yourself:

Schneider, Eric D. & Sagan, Dorion (2005). Into the Cool: Energy Flow, Thermodynamics, and Life, The University of Chicago Press. [covers a lot of these hypotheses from the standpoint of non-equilibrium thermodynamics and energy flow.]

Morowitz, Harold J. (1992). Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis, Yale University Press. [A bit older than the Morowitz reference I gave, but full of much more details at the molecular level.]

There is also a rich literature on RNA-world for the origins of both enzymatic action and autocatalysis pre-proteins. But there is still a gap in understanding the precise mechanisms involved in coupling the origins of a replicable genetic code and the early metabolic cycles. Some recent work on coupling early bi-lipid membranes, ribozymes, and minimal autocatalytic cycles involving polypeptides on pyrite surfaces driven by sulfur REDOX reactions (e.g. deep thermal vents today).

If you have recent literature to the contrary please advise.

---------------------------------------
@D. Aaron F.,

I am no expert on nuclear plant operations (though I was on a nuclear sub in the Navy!), but it is my understanding that even in the worst case scenario, where all of these plants fail containment, the ensuing radiation contamination would not be much greater than the Earth has experienced several times in the past due to losses of ozone (for example). In fact, I have read an analysis that suggests the increased radiation (of course at some distance from the source of the contamination) could increase the mutation rates in many species which would provide much more likelihood of beneficial new traits!

Our visions of a nuclear contamination meltdown come mostly from conceptions of Armageddon (nuclear winter) scenarios of when the bombs (very dirty by comparison to nuke plants) fell. That kind of scenario would, indeed, be devastating. But if we look at Chernobyl, as an example, we don't see the same kind of simple radiation die-off. In fact the area surrounding (at a distance) the disaster is quite alive. There are, of course radiation-related diseases and mutations have been reported. But the level of harm seems no greater than what we would expect from a natural selection force.

For my part I remain skeptical of claims that all of these plants would be left decommissioned and subject to melt-down, for starters. And those that might, I remain skeptical that it will result in annihilation of all life around. I await evidence to the contrary!

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@Paul H.,

That is the extent of evolution though. There is no plan to produce a super-species of humans.

I don't think I implied a "plan". That would imply an intelligence-based teleology. There is no implication of a plan in recognizing a trajectory and pattern (of emerging levels of organization) in universal evolution. Even some evolutionists are getting comfortable with talking about a telenomic purpose without needing to imply a supreme creative intelligence driving the process.

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@Ulises,

Thanks for the link and suggestion.

Bioquestions and the mechanical answer, by Didier Newman.

I read most of the first chapter. I have to say the very first sentence is a less than an up-to-date premise, verging on false. The rest seemed a rambling musing without any clear claims or evidence cited. Put bluntly, I didn't grok his arguments.

Perhaps you can elucidate based on your complete reading.

-------------------------------------
@Tom,

We simply refuse to accept the idea that we're nothing special and have our time on the earth like all other species and then we're "shown the door."

Is there really disagreement? I have been making the case all along that, so far as biology is concerned, Homo sapiens is destined to go extinct just as any other species.

But extinction does not necessarily lead to the end of a genus. There have been numerous previous species of Homo that have gone extinct but the underlying adaptability of the genus seems quite robust, having produced a species that is able to inhabit nearly every nook and cranny on the planet (except Antarctica) even before technology as we know it. All of the paleo-anthropological evidence points in this direction.

My conjecture (science fiction if you will) is that, given the evidence to date, our species, making it through a bottleneck will go extinct but before doing so give rise to a new (or even several new) species that will be more fit for that future environment. Mankind as we have known ourselves (and failed to understand ourselves adequately) will be gone, replaced by a "better" version of the genus. My further conjecture (science fiction) is that what that means is a species that is much more cooperative, empathetic, and communicative than our current form. Those traits will be selected for because it is cooperation and integration that has ALWAYS in the past been the solution to survival in a radically different environment and the emergence of new organization. Since this has been the pattern in the past evolution of life and supra-life on this planet (as we are now coming to understand) it seems perfectly reasonable to me that it will be the pattern of the future as well.

Now I make no claims whatsoever that this is guaranteed, only that it is at least as likely an outcome as the complete extinction scenario for Homo. For those who choose to believe (and it can only be in the realm of belief since we've never run this experiment before) that the state of the environment will get so bad that essentially no life forms comprised of more than a few cells will be able to survive, then, of course, no other conclusion than total extinction is warranted. My own view is based on the results of prior die-off events and the resulting post-die-off radiation of biodiversity (c.f. The P-Tr Event). After every such event the new Earth environment was quite different from the prior state. Those species that retained the greatest level of adaptivity and evolvability made it through to give rise to wonderful new biota.

So, I argue, the evidence so far suggests a more positive outcome than ultimate gloom-and-doom. In the end it is all speculation, of course. But I have to say, I think my scenario gives us hope that whatever else may come, the representation of sentient life on this planet could very well go on and thus provide a chance for wonderful things yet to come. That is an idea that can motivate positive work in the here and now. I would admit, it is what keeps me going.

George

Reverse Engineer

No, nothing recent from my end George.

I'm a Proof is in the Pudding sorta guy. When somebody creates a self-replicating organism from just organic substrates, I will sit up and take notice.

Has anyone done such a thing yet and I missed it?

Until that has been accomplished, you just make a Leap of Faith that it can be. It is just a belief system George.

RE

George Mobus

@RE,

Perhaps a lot has been going on that you have missed! Such as synthetic genomics. Or look at RNA world.

No one has created a self-replicating bug just by throwing a bunch of organic stuff into a bottle and sparking electricity in it. But they have created replicating bugs/yeasts with artificially constructed genomes. They have demonstrated the effectiveness of ribozymes in protein synthesis. Most of the pieces of an extremely complex puzzle are in place.

Don't you think you should take a look at the literature before discounting something just because you have not seen some final product that you judge as the only viable demonstration?

In any case, does the elimination of this one claim invalidate my post?

George

Reverse Engineer

I'm aware of Craig Venter's work. Lander's also. :)

Thing is, creating a synthetic genome is a Sentience directed process, aka it takes Homo Sapiens in a laboratory with fabulous Oil Age materials and equipment to do it. It doesn't occur randomly or spontaneously.

To make a thermodynamic type argument, like using the analogy of the spontaneous organization of a Tornado or Cyclonic Storm as Paul did, you have to show this can occur without directed action by an already sentient being, us.

Not only do you not have any demonstration of how this can occur, far as I know (you will correct me I am sure if I am wrong) there is not even a proposed mechanism for such a spontaneous self-organization of just DNA itself, forget about the pairing with RNA and protein coding issues.

The biggest Leap of Faith is in the Information Coding. What Venter is doing is taking ALREADY KNOWN 3 base pair sequences which code for specific amino acids and creating an artificial genome out of it.

How did that coding come to pass spontaneously on a thermodynamic level? Propose a mechanism for that. Inquiring minds want to know. :)

RE

George Mobus

@RE,

The answers you seek are in the reading list I provided. I think you should take a look.

George

Reverse Engineer

I took a look George.

The RNA hypothesis is an interesting one, but far as I could find there was no explanation of how the coding could occur spontaneously.

Rather what I did find that there is dispute over whether the RNA could have held together or polymerized in the absence of energy activation from ATP.

""Molecular biologist's dream"

"Molecular biologist's dream" is a phrase coined by Gerald Joyce and Leslie Orgel to refer to the problem of emergence of self-replicating RNA molecules, as any movement towards an RNA world on a properly modeled early Earth would have been continuously suppressed by destructive reactions.[47] It was noted that many of the steps needed for the nucleotides formation do not proceed efficiently in prebiotic conditions.[48] Joyce and Orgel specifically referred the molecular biologist's dream to "a magic catalyst" that could "convert the activated nucleotides to a random ensemble of polynucleotide sequences, a subset of which had the ability to replicate".[47]

Joyce and Orgel further argued that nucleotides cannot link unless there is some activation of the phosphate group, whereas the only effective activating groups for this are "totally implausible in any prebiotic scenario", particularly adenosine triphosphate.[47] According to Joyce and Orgel, in case of the phosphate group activation, the basic polymer product would have 5',5'-pyrophosphate linkages, while the 3',5'-phosphodiester linkages, which are present in all known RNA, would be much less abundant.[47] The associated molecules would have been also prone to addition of incorrect nucleotides or to reactions with numerous other substances likely to have been present.[47] The RNA molecules would have been also continuously degraded by such destructive process as spontaneous hydrolysis, present on the early Earth.[47] Joyce and Orgel proposed to reject "the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides"[47] and hypothesised about a scenario where the prebiotic processes furnish pools of enantiopure beta-D-ribonucleosides.[49]"

Still no closer to taking that Leap of Faith with you across the chasm of spontaneous life generation. ;)

RE

Aboc Zed

i don't remember if george recommended the book or i heard about it somewhere else but I found

"What is Life?: How Chemistry becomes Biology"

by Addy Pross

a good read as a conceptual overview of issues around transition from inorganic matter to LIFE.

amazon link

http://www.amazon.com/What-Life-Chemistry-becomes-Biology/dp/0199641013

i found this pdf on pre-boitic chemistry and reactions screening interesting as well

http://www.google.ca/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=1&cad=rja&ved=0CCkQFjAA&url=http%3A%2F%2Fwww.mdpi.com%2F2075-1729%2F3%2F2%2F331%2Fpdf&ei=KZ2cUozfE8X0kQfUw4B4&usg=AFQjCNGXGCFGmVYhHOxvEx8G_9uFSEf2RQ

Gavin Taylor

Our incredibly quick complex insanity has nothing to do with the other types of nature, because ours is one of "ideology" or whatever other bad word. To include cultural complexity you're now talking structures of language, thought, perception as well as everything else.. way out of anyone's intellectual league. It's not linear stuff, so it will never be understood as linear.

When I was about 12 I asked myself whether people would look more the same or more different over time. To get into that we're talking about not just evolutionary and visual preference and other aspects in individual selection and tribal extinction, but all the other factors too, and my question even wanted to keep going along without a specific endpoint. I now realize I struggled because I asked an impossible question!

And the types of narrow-mindedness ever-present here academically as well as in Internet privacy (http://en.wikipedia.org/wiki/Global_surveillance_disclosure#December) and politics (http://www.youtube.com/watch?v=mChqQhRhwwY) will continue to fail to explain anything useful as regards to Near-Term Extinction without the whole range of spiritualistic, nihilistic, critical and analytical modes and items of discussion. Isolation or externalization, in thought, is death. Everything is The Problem. There is no simple fix. Self-preservation continues to declare itself the opposite of human species survival today.

----


(Response to someone else's comment about the state of the world)

It's not like anything much is going to happen "in time", we've been at it for so long and only saying "maybe we'll be too late" now. The penny's gotta drop sometime. People say they don't believe in climate change, as if you could pollute everything and have no consequences, no correlating patterns ever - Shanghai closed some schools and businesses recently because of the smog, they have been going beyond where people have to wear masks all day outside. These people are insane, and nobody even points it out in the mainstream. The only reason for that is money - the children now getting cancer, all through to the elderly, will yield more money after they're dead. We treat people like animals now. The farmers are ravenous wolves, like we are all ravenous wolves of the global economy. We all preach this death, unknowingly, unconscious, but we do. We do it by living, which is a message clear as any other unwritten unspoken one. We don't educate children, we show them what it means to be bullied, we set the stage for this horrific ride. It's got some nice visuals but it's complete evil underneath. Every politician in the world knows this, they don't understand it within but they know it. Every activist knows it but I'm not sure they understand. These are all things which contribute - where is the anger? Where is the support of parents, the churches, the people making these tools of oppression like video games? Where are their minds? Where is their consideration? Their mind is at the back and their isolation has the crown. Escapism is the only mental health disease in the bigger picture. Mental sickness is health for the society where a middle class needs to be terrified into keeping their jobs so they don't end up in ghettos. People should be standing up for other people in every case, but there is so much confusion that it turns again to the engineered primitive hatred, like TV is the pornography of the visual and war is the pornography of violence.

When will we raise critical thinkers that can even challenge the authority of the world they live in? Only when it becomes financially profitable in the short-term. Humanity can do anything in theory, man is fragmented God - but not under the tight grip of the worship of money, with our high priests we watch from our TV caves talking about when there might or might not be a problem if we upset the gods of the financial system. In reality, everything is a system, but human beings are frightfully avoidant of this inside our well-programmed culture of fear.

This is far more than a violent conflict being played out in isolation, on some imaginary battlefield where oil companies are one/the end of it. This is everywhere. Earth is the battlefield, in a vast universe of possibility. Change doesn't happen until a need arises. While people are placated by the system, the only thing that will happen is this shaky voice of the scientist in journalist-padded-and-prepared articles telling you the world might end if we continue to be happy with this world. Human beings can't stop needing to be happy. There is nothing clearer than the fact we're already completely fucked. Genocide is one partial solution and in fact inevitable to continue the Western way of life anyway - it WILL happen, these people WILL be murdered "either way". But life in this universe follows a very scientific chain of cause and effect: the most likely thing BY FAR is that we keep to the comfortable, known process of human life. Any true, any serious and mature and non-emotional solution to The Problem now includes a complete reinvention of what human life is. Full stop. The seas will rise for thousands of years. The climate will burn the plants from the enormous self-perpetuating "myth" called thermodynamics involving present mass methane releases.

And we think we have an answer - it's a very $$$$$$$ *maybe* maybe.

And so we come back around, as our brains are structured, to our own self-preservation in this irrational existence. The ingrained individualistic teachings of our world draw us to say that we might as well enjoy "this" while it lasts. And you'd be making a very scientific decision for yourself there.
[Moderator edit: removed offensive language - first warning.]

Gavin Taylor

I'm not sure what to call it, but here's part of the Illuminati's mathematical explanation for the Big Bang and black holes, moving towards a true TEO achievable today:


Hyperreality - Hockney, Mike (749.25KB)
http://www.sendspace.com/file/88fkrn
The Noosphere - Hockney, Mike (1.74MB)
http://www.sendspace.com/file/a9s1qg
Julian Jaynes - The Origin of Consciousness (2.98MB)
http://www.sendspace.com/file/froat4


also see
http://armageddonconspiracy.co.uk

Gavin Taylor

If we're truly Questioning Everything, then we should also be aware of the emotional rationalizations and escape involved. The Hope presented at the bottom of this article here for another form of life on the planet is far-fetched as soon as you take in the rising sea levels and superfast mutations. (Not to mention the psychologically suspicious item of wanting to carry on a roughly similar life form to that of our own). 150 000 years, the time we evolved in, was additionally from the base of a stable climate and ecological platform, the land of which we've replaced almost half of (http://news.mongabay.com/2013/0520-olson-biosphere-conservation.html). The trees are rotting from the inside on account of pollution which has an additional 30-40 year lag after our machines stop, and it's trees that provide for example a basic role of nurturing insects.

There are other points to go to from here, personally, spiritually. (And that, in some sense, is what guymcpherson.com has become about). Did you know, the universe is made of mathematics? It means what we are, this "life force", can never die. The universe is actually immortal, and the Big Bang was a particular spatial type of "life force". There was something just as powerful behind it, mathematics is very clear about this. There are people in this world that know far more, and I sort of wish I was one of them. There are also other civilizations, other lifeforms in this universe, that will survive because they didn't have sociopaths or the petrodollar or any need to control each other at all, weren't isolated with no guidance from other species or nations or civilizations. Everything that happened to the human world, which begins and ends nowhere in particular, is wholly specific to parameters like the size of the Earth, the amount of water and oil. We act out such simple things in light of this, like geopolitics i.e. war for oil another country has, which is ridiculously silly and primitive when you zoom out. We truly are a lot more complex even in our bodies than all of this, and we are laying claim to a heritage much richer than our fantasy world of human dramas - there's just so much to love and respect about the universe and its immense power.

Some videos like this can really change your day sometimes
http://www.youtube.com/watch?v=Hu5oaty0uJM
http://www.youtube.com/watch?v=irOsHLay9X8
http://www.youtube.com/watch?v=BbWWT3X8Ebo&list=PLHLAJCWpWqEka1Vk5EuBVnQE_6-qyAP-K

Christian Mobus

If traditional evolutionism is correct, why then would our consciousness be such a wonderful and misunderstood enigma? Wouldn't we have evolved as other mammals have, only needing the essentials of life? No other creature has expanded on their technology as humans have. It seems absurd to imagine a chimpanzee driving a BMW while talking to a business associate on a cell phone. Isn't this what evolution is suggesting? That we came from the "animal kingdom" and we've "evolved" from nothing?
Why are we so inventive and complex? Why do we care so much why we're here? If we humans are so rudimentary as evolution suggests, why are we so different from other species of Earth? Opposable thumbs! A larger brain! Did we really need these things to survive? Did these genetic mutations give us a REAL advantage over other species? Were they necessary developments for progress?
My point is.. What's the point?
If evolution is correct, then we are all just a bunch of dumb apes chasing our receded tails.
It seems there's more to the story than that. What makes us so incapable of satisfaction? Why do we need more when we have enough? The only other organisms that behave as we do are viruses. Reproducing past the limits of our own sustainability. Destroying our host planet by leeching off its abundance. Our overpopulation and insatiable appetites are what's eventually going to be our undoing.
There may be (and I'm hopeful you're right, George) a sort of sapience that's going to be the knight in shining armor whom will take our genotype past its current parasitic installation. It won't be over night.
The powers that be ($$$) will resist with every effort, the evolution into a truly harmonious relationship with Earth. Maybe, we're searching in the wrong timeline. The wrong "trajectory". Just because we're taught something in school, it doesn't make it factual. I should say, just because we're NOT taught something in school, it doesn't mean it didn't happen.
There seems to be a lot of discourse regarding lost civilizations and lost "higher" technologies. All of which seem to be ignored by the current academia.
If all of Earth were a lobby in a building, I would yell out, "WHO'S IN CHARGE HERE?". No one knows! We really are the blind leading the blind. No wonder why we're in the toilet.

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