Closer to Creating Life in the Laboratory

[Cracker Funk]

mussoman, to me, it's the Trek equivalent of midichlorians. We were perfectly happy just accepting that The Force just was. We didn't need a scientific explanation for it. escher touched on the real reason why there are humanoids on other planets -- because it makes production incredibly less expensive. Also, I think Trek would be really boring if they didn't spend most episodes interacting with human-like alien species. So, we'll just accept that it is; no need for a psuedo-scientific explanation.

escher -- your suggestion that bipedalism is somehow an advantageous trait is actually the exact reason why I hate this particular episode of Trek, because it promotes the same line of reasoning. I think it's perfectly natural to see the dinosaurs as the creatures that ruled the world for a really long time, and if it weren't for a giant rock colliding with Earth, they'd still be here (as dinosaurs, not birds). And now, it is humans who rule the world. What do humans and (a small handful) of dinosaurs have in common? Bipedalism.

This is a very common misunderstanding of how evolution works. In my experience, even science nerds have some pretty big misconceptions regarding the process of evolution. And perhaps the biggest hang-up comes from the phrase "Survival of the Fittest". It's very easy to think of ourselves as the apex of evolution. It's very easy to think of evolution as a process of constant improvement. Each new iteration of a species is more fit than the previous version, and humans are obviously the most highly evolved.

But that's just flat-out wrong. There are no genetic traits that are better than others. There is absolutely nothing inevitable about evolution. It is random and chaotic, and the traits that will be selected for in one environment will be selected against in another.

If bipedalism is so great, then why have so few species used that form of locomotion? If it were such an advantage, shouldn't it be more widespread? As far as energy efficiency is concerned, our human gait is actually incredibly inefficient. And think about this -- if climate change hadn't resulted in the drying-up of Eastern Africa, some 5 million-ish years ago, humans wouldn't be here.

And that is because bipedalism is NOT advantageous for a primate living in the forest. It's only when the forests of East Africa receded, leaving behind vast grasslands, making it advantageous to walk upright. Food became more sparse, and longer distances needed to be traveled. And seeing as how dependent an ape's young are, the food needed to be collected and brought home. That requires walking upright, so that the hands could be free to carry food.

Bipedalism would not be advantageous for a whale. Or a mosquito. Or an alligator. Or a cockroach. Or a shark. Or a mouse. And those creatures have been around for a much longer time than humans and dinosaurs combined, and they've remained virtually unchanged.

Evolution does not naturally move towards any particular traits. There are no genetic traits that are better than others. The only thing evolution does move towards is variation, and change. And it always gets that. What's good for one is very infrequently good for another, and in addition to that, you must recognize that in order for a change to take place, there first must be a genetic mutation in place, and those are 100% random.

 

[escher]

Bipedalism is incredibly advantageous because it frees up two limbs for tasks other than locomotion. But it's long-term advantageous, and as you pointed out, evolution is random and chaotic. Unless the environment and other factors push a species towards bipedalism, they'll remain stuck in their local minimums because they'd have to go through less-advantageous forms to get there.

I run evolution experiments in simulations, I'm very well-versed in how evolution works.

<mad_scientist_voice> I have watched order arise from chaos with my own eyes! </mad_scientist_voice>

(Seriously, I have. It's really something to behold.)

 

[Cracker Funk]

It's not even long-term advantageous. And the dinosaurs that were bipedal didn't even use their forelimbs. It's advantageous for US, because it frees up hands for something other than locomotion. And hominids are the only family, in the entire history of life on Earth, for which this is the case. There are WAAAAAAAAAAY more species for which it would not be advantageous. Humans are not the apex of evolution. We are not more highly evolved than any other species. What works for us would not work for a shark, and sharks are doing just fine. In fact, they'll probably out-live us.

 

[rayw]

Evolution does not naturally move towards any particular traits. There are no genetic traits that are better than others. The only thing evolution does move towards is variation, and change. And it always gets that. What's good for one is very infrequently good for another, and in addition to that, you must recognize that in order for a change to take place, there first must be a genetic mutation in place, and those are 100% random.

Further complicating the process is that not only does a single incidence of a specific random advantageous mutation need to take place but several of the same variations must appear at the same time and in the same location in order for a single mutational variant trait not to be simply over-bred right back out into the average no matter the advantageous benefit to the individual.

Humans are not the apex of evolution. We are not more highly evolved than any other species.

Heh heh heh. I'm waiting for this principle to come full circle on two different levels and come biting us on the @ss.

One, if we manage to use our superior intellect and tool making abilities to basically begin another mass extinction, and I believe a good argument could be made we're already well on our way, which includes ourselves then just how "superior" are we?
Great. We burned ourselves out in less than a million years. Effing brilliant. We're a bunch a GD geniuses. Way smarter than those mice scurrying about... for tens of millions of years.
The current humanity model is "superior" to that of the mice and rats, right?

Two, any particular reason why the capitalistic consume-all-resources model is better than one that discourages rapid resource consumption? Personally, I'm not so sure all this "freedom" to do this and that is going to work out too good over the next few hundred years, let alone few thousand or tens of thousands or hundreds of thousands of years.
Thinking of humanity just one million years from now is likely "beyond reason" for most people.
Humanity+hundred million years would be considered absurd, right? Right?
Our current social model is "superior" to hunter-gathering, rife with high infant mortality, low longevity, and low quality of life, right?

D@mn! My iPad mini needs recharging! Now I gotta use my ancient iPhone4 to communicate. Bugger!

 

[Cracker Funk]

Further complicating the process is that not only does a single incidence of a specific random advantageous mutation need to take place but several of the same variations must appear at the same time and in the same location in order for a single mutational variant trait not to be simply over-bred right back out into the average no matter the advantageous benefit to the individual.

No, that's not how Natural Selection works. Which again, this really is one of the least understood things that everyone thinks they understand. I've personally spoken to professional geneticists who didn't fully grasp how Natural Selection works (which makes sense, because Natural Selection is a bigger picture type of thing, whereas genetics involves looking at the smallest picture possible).

To clear up your misconception, rayw, we need to discuss genetic drift. And the most popular case-study to cite is the relationship between sickle cell trait and malaria.

The vast majority of genetic mutations are meaningless. They neither hurt nor help. With enough mutations grouped together, you get a new genetic trait. Some traits are beneficial, some are harmful, most are inconsequential. A genetic trait that is inconsequential will just kinda hang out. It won't be weeded out, nor will it flourish. It just kinda drifts about. But by the simple act of mating, an inconsequential trait can become present in numerous individuals in a gene pool.

One such example would be sickle cell trait. If an individual has sickle cell trait, their blood cells will burst, when their acidity level rises too high. This makes it very difficult (and painful) to run a marathon. But for every day normal living, they're fine. It's really not a life-threatening thing, and plenty of people live with sickle cell trait, without any significant problem.

You'll have sickle cell trait if one of your parents had sickle cell trait. But if both of your parents had sickle cell trait, you're gonna have sickle cell anemia, which is a much more extreme version of the same problem. Walking up a single flight of stairs can raise your acidity level to perilous levels.

Sickle cell anemia is bad enough that it works as a limiting factor on how many people sickle cell trait can spread to, within a given gene pool. But sickle cell trait is harmless enough that it'll never completely be weeded out. So the trait remains in the gene pool, just kind of drifting around.

Enter malaria, stage left. When malaria attacks a red blood cell, the acidity level rises. In an individual who does not have sickle cell trait, the malaria spreads like wild-fire. In an individual who has sickle cell trait, the cells that malaria attacks burst, instantly killing the malaria virus.

Now, all of a sudden, that genetic trait that didn't really mean much, and has just been drifting around, now it's a HUGE advantage. Sickle cell trait and malaria both originated in Western Africa, and that would explain why African Americans have a much higher incidence of sickle cell anemia than any other American population. It is because there was once a time when that trait was advantageous.

But the point I make is this -- sickle cell trait didn't just randomly evolve, as a response to malaria; it was already there. Random mutations come first, genetic drift happens for a while, and then environmental pressure is the final step of the process.

 

[Jack Lynt]

Wow, thanks for that great explanation of genetic drift and sickle cell, Cracker. You made it so even I could (I think/hope) understand it.

I really appreciate being taught and reminded that evolution doesn't work towards anything and that this or that trait isn't necessarily generally advantageous. I think those of us who have that natural urge to want to think that humans are at the apex of evolution or that they (humans) are "advanced" life forms, or whatever, need not despair at the knowledge that it ain't so...as far as evolution is concerned. For one thing, it's a mistake to personify evolution like I just did in the preceeding statement, after all.

No, evolution doesn't give a poop, just like it doesn't give a poop about anything. And, there isn't even an it to begin with. But, that doesn't mean that we cannot say, well, we are humans and bipedalism is of advantageous value to us...because we are we. Bipedalism and having free hands may have helped or contributed to our brains getting larger and smarter, for example, which made us what we are, and we like what we are. We're glad that we got the chance to be us.

Forgive me if I'm mixing things up. I think I've been hearing different things about what came first and encouraged the selection for what (free hands, bipedalism, language, large and smart brains etc). And if I'm not mistaken, these are not settled questions yet, anyway.

No, evolution and sharks couldn't care less about bipedalism and large, smart brains. But we, being what we are, do value our large brains and our smarts and our free and dexterous hands etc. That's perfectly reasonable and no one needs to be ashamed of thinking or saying so. You are human, after all, and humans will value what is valueable to human life...despite there being no Evolution or Nature that cares or has designed us with "apexness" (sorry) in mind. But, whether Evolution designed things to be the way that they are, or whether it gives a crap, which it doesn't and which it is not capable of, anyway, it is human nature and the human prerogative to find and to give meaning to what it values for itself. I guess we're the only species which is quite so self-aware that it can say something like, gee, I'm glad and it was advantageous that East Africa dried up, that our ancestors were forced to move out onto the savannahs, that walking upright was selected because it allowed them to see over the grass and watch for predators and prey, which in turn freed up their hands even more than before, which may have led to selection for a brain which could opimize the use of those hands and the new things they were finding to do with them, which may have selected for a brain that eventually became capable of languange (sorry if that's not quite how things went/if I'm talking out my you-know-what). Those things can be true for us subjectively, from our human perspective, even if as far as evolution goes, those things were all chance and without intention and of no concern to any objective view of the biosphere or what species differentiation has occurred or resulted by the workings of evolution.

Keeping in mind, of course, Cracker's warning to not confuse that with, well, design...isn't that what it really comes down to? There is no design, no purpose, no plan, no direction, no progression (as in towards progress) as far as nature is concerned (oh boy, not meaning to personify nature!).

Did I just hear or read the other day that the bacteria that lives on and in our bodies far outnumber the cells of our own bodies? Is that right, or am I imagining that that's what I heard? Anyway. No surprise. I guess I knew or sort of knew that, or would have had to guess that. But anyway, isn't it amazing? I mean, then, when you start thinking about life, and our lives on the cellular level, and looking past, or beneath, so to speak, the fact that we are complex organisms who happen to be sentient, but instead focus on the us who are a collection of all these cells, and these cells that make us us coexist so closely with all these tons of other microbial life forms...some in cooperation, some in competition, some in mortal combat. Well, I guess I'm not really going anywhere with this, nor does it have much to do with the above, I suppose. It's just, these cells are largely unware of the beings, us, that they make up. And the cells that are "along for the ride," sort of, are even less aware of us, except, I suppose, as a food source. And of course they are unaware of us because they are pretty much unware of everything, aren't they?

In a way, I suppose, that's like trying to not see the forest for the trees. Still, isn't it interesting to imagine this little universe going on that is largely under our radar...except, unhappily, when it causes us trouble and grief?

Again, sorry, not really going anywhere with this either, but isn't it interesting what we're hearing about the so-called junk DNA, or how about the epigenome? We were hearing that there was this junk DNA that was maybe just along for the ride or who knew what, but...maybe, not so fast; things might be more complicated than that.

A quick search found this very interesting article:

The Wall Stree Journal: 'Junk DNA' Debunked

 

[escher]

Cracker Funk and richy speak truth, although I maintain that bipedalism gives a serious advantage to those organisms that evolve it, both in freeing up limbs for flying/tool use and, in the case of humans, allowing for the development of the ability to both run and breath heavily simultaneously.

Not planned, of course. It's weird how many people think evolution has some kind of guiding hand with a target in mind.

I recently finished up the initial development of a generic chromosome and DNA mixing template in C++. I'm using it to cross-breed neural network brains.

 

[mus]

midichlorians make me sad

 

[Jack Lynt]

I recently finished up the initial development of a generic chromosome and DNA mixing template in C++. I'm using it to cross-breed neural network brains.

Those experiments that you do sound really interesting, Escher.

midichlorians make me sad

They make me sad and in a way they don't. What I think I respect about what it seems Lucas was trying to do was take the force from a fantasy element and make it a scifi element. Am I happy with the end result? No, not me either. But, I can respect the sentiment, too. I suppose Lucas may have spelled exactly what influenced him and what he intended by the force in the first films over the years. But I'm not going to try and google that now. What matters to me is that whatever he has said, the force of the first films owes a lot to ch'i/qi/ki. I mean, it seems that the force is largely ch'i, only with mad telekinesis and clairvoyance skills and such. Oh okay, I can see by a quick look at the Wikipedia page that that is an uncontroversial statement, like I thought. Anyway, ch'i and the force are fantasy elements. But by introducing microorganisms that generate the force Lucas, apparently, was trying to give the force more of a scifi character. Not very satisfying. But, I can, on some level, appreciate that.

 

[AudioPostExpert]

As strange as it may seem, this statement is false:

...evolution has been 100% proven.

While this one is true:

Einsteins theory of relativity was also never proven either.

As has been mentioned/implied, most of our (the general public's) experience of science is based on how science is reported in the media. The problem with the media is that it presents scientific research in easily digestible bites and in so doing usually simplifies it to the point of inaccuracy.

The simple fact is that science is based on relatively few absolute rules or truths (laws), the majority of scientific knowledge is based on theories, which represent a probability of absolute truth. The probability of a scientific theory being true depends on how much supporting evidence there is for that theory and the general consensus of the international scientific community. The theory of evolution for example has a great deal of supporting evidence and is accepted by the overwhelmingly by the scientific community. Einstein's theories of relativity are a little more complex because they appear to contradict another theory of physics (Quantum Mechanics) and for over 60 years the world's top theoretical physicists have been trying to find a new theory which explains and unifies these two theories, so far without success. Nevertheless, in today's world we rely on a fair amount of technology which relies on one or other of these theories.

A scientific theory is essentially nothing more than a man made model, designed to aid our understanding of how and/or why something works. Some few scientific theories are certain to be true, some others are known to be false but represent the best understanding we have currently and many other theories lie somewhere between these two extremes. So each theory has to be taken in context and on it's own merits. This actually impacts my work on occasion. The Nyquist/Shannon Theorem explains how/why digital audio works but there are many who work professionally with audio who don't understand this theorem and believe certain things about digital audio which cannot possibly be true, their argument being that their observations are more valid than a theory. In the case of digital audio they are wrong because unlike many theories which were developed to explain an observable phenomena, the Nyquist/Shannon Theorem was developed first and then 20 years later the earliest digital audio technology was developed based solely on this theorem. So if the theorem is incorrect digital audio could not exist. This leads to some interesting discussions/arguments within the audio community!

There is an old saying and sometimes very unfortunate truth about Hollywood: "Never let the facts get in the way of a good story!" Supposedly historical films like U571 and many others have been heavily criticised for doing exactly this.

G

 

[Cracker Funk]

Some few scientific theories are certain to be true, some others are known to be false but represent the best understanding we have currently and many other theories lie somewhere between these two extremes. So each theory has to be taken in context and on it's own merits.

I can understand how one would think that, but that's simply not true. Ironically, you mentioned how much of a disparity there is between how science is reported to the masses, vs. how it is understood by those who actually study it. The definition of what constitutes a "scientific theory" is WAY misunderstood.

It's not a scientific theory unless it is WIDELY accepted. That's not so say that it's not open to debate, but there is absolutely no scientific theory that is known to be false, or even one that lies somewhere between fully-accepted and false.

Also, a scientific theory and a mathematical theorem are not one and the same. A theorem can be PROVEN. A scientific theory is pretty much proven, but hey, you never know, we might some day discover that gravity is actually random.

Also -- escher, I second what richy says -- your line of work sounds really cool. Big ups to you for that!

 

[escher]

escher, I second what richy says -- your line of work sounds really cool. Big ups to you for that!

Hah! I wish I could get paid for that, but it's only a hobby. My day job involves writing c# code to process billing files, most of which appear to be designed by drunken leprechauns having a real bad day.

 

[AudioPostExpert]

It's not a scientific theory unless it is WIDELY accepted. That's not so say that it's not open to debate, but there is absolutely no scientific theory that is known to be false, or even one that lies somewhere between fully-accepted and false.

OK, you're right, that is certainly not my understanding of a theory. For example, Quantum Mechanics contains a number of competing theories (String Theory, Superstring Theory, M-Theory, et al.) none of which have full-acceptance and all of which are fully-accepted to be false under certain circumstances (high energy levels for example). Einstein famously spent many years trying to prove certain tenets of Quantum Mechanics were false, only to be proved wrong by subsequent experimental evidence.

The example of gravity is a particularly good one. Newton's Law of Universal Gravity is known to be false and has been known to be false for over a century, in fact it is only true within a quite limited range of gravitational field strengths.

Also, a scientific theory and a mathematical theorem are not one and the same. A theorem can be PROVEN.

I agree they are not the same thing but their attributes are similar, which leads inevitably into a philosophical discussion! The 3 example theories I quoted above are all provable mathematically. However, these proofs depend on a branch of mathematics which employs abstract constructs (such as Hilbert Spaces) which along with many/most other mathematical theorems fall under Godels Incompleteness Theorem, meaning they can never be proved. Not quite as black and white as it at first appears!

A scientific theory is pretty much proven, but hey, you never know, we might some day discover that gravity is actually random.

I disagree, a theory can be widely accepted and believed to be true but by definition is not proven. Some scientific theories are backed up by so much evidence in favour and so little against, it's virtually inconceivable they are incorrect but others are far less probable and some are known to be at least partially false. The current theory of gravity is at the very least incomplete and possibly even wrong, which is why we currently have so many different competing quantum gravity theories!

So I still content that a scientific theory represents a usable model for understanding truth and a probability rather than a certainty of absolute truth.

G

 

[Jack Lynt]

Wikipedia: Scientific Theory

It's unfortunate, but understandable, that when many people hear the theory of evolution described as "the theory" they conclude that the scientists who call it that themselves "admit" that it is "not a fact," but, "just a theory."

Isn't it just a confusion of semantics? To call something "a theory" in science, a scientific theory, is to use, really, specialized language, as the sciences are want to do. To call something "a theory" colloquially is pretty much to say that something is "just" an idea, or, just speculation...which sounds quite a bit lot like an hypothesis (not even a scientific one) to many people, I'm sure.

Wikipedia: Hypothesis

So, it might help if more people knew and accepted the fact that the theory of evolution is "...a well-substantiated explanation of some aspect of the natural world that can incorporate [a crap-load, a voluminous body of] facts, laws, inferences, and tested hypotheses.”...," not "just" an hypothesis, and not "just speculation."

It's a word game, sort of, and some are innocent in simply not being aware of the difference, and, no doubt, some who are hostile to the theory of evolution exploit that confusion for less than innocent reasons and purposes.

. Some scientific theories are backed up by so much evidence in favour and so little against, it's virtually inconceivable they are incorrect but others are far less probable and some are known to be at least partially false.

Some teacher in my life, I think it was the professor of a Zoology class I took, said almost that very thing about the theory of evolution. =)

 

[escher]

Gravity exists and we have a theory of how it behaves.
Evolution exists and we have a theory of how it behaves.

I once hooked up asexually-reproducing feed-forward neural network brains to run single-celled organisms that ran around in a simple simulated world (2D, randomly-appearing plant life). The world started with randomly-configured brains, so most of them just twitched in place until they starved to death, but there would be the occasional organism that would randomly "bite", and eat, and survive and reproduce. Reproduction was just a copy of the brain, with a random chance of mutation for each neuron and axon in the brain. From that pure randomness came crawling, and from that came crawling and turning, and those dominated the world within two generations. That's when the carnivores really got a foothold.

When you have a self-replicating system with a random chance of random mutation placed in an energy gradient, order arises naturally from chaos.

Can't wait to get the new cross-breeding LSTM neuron-cloud model brains up 'n running in a new 2D world...

 

[AudioPostExpert]

Isn't it just a confusion of semantics? To call something "a theory" in science, a scientific theory, is to use, really, specialized language, as the sciences are want to do. To call something "a theory" colloquially is pretty much to say that something is "just" an idea, or, just speculation...which sounds quite a bit lot like an hypothesis (not even a scientific one) to many people, I'm sure.

Absolutely. A scientific theory is a complex structure. It must have a number of attributes to be a fully-accepted theory, among them repeatable evidence, peer review and scientific consensus. This represents the great strength of science as a belief system, it's requirement to question and challenge itself at any and every level. Scientists have almost as much to gain (and in some cases more to gain) from disproving a widely-accepted theory as from inventing or discovering an new one. This great strength is exploited as a weakness by some who have their own agendas. For example fossil fuel based industries who exploit any hint of scientific questioning of climate change to "disprove" their business contributes to the problem or of course religions who historically ostracised or even stoned or burnt at the stake any questioners.

Gravity exists and we have a theory of how it behaves.

This is what I was trying to explain: Few, if anyone, would dispute that gravity exists but we don't have a theory of how it behaves! Or rather we have two different, apparently mutually incompatible, theories explaining how gravity behaves under different circumstances and then 15 or so candidate theories which attempt to describe how gravity always behaves, all of which are incomplete and contain serious and currently unsolved inconsistencies/problems. BTW, what makes the search for a complete theory of gravity so interesting is that a complete theory of gravity appears to be the final step required for what is called the "Theory of Everything", the theory of how all the forces in the universe combine and behave.

G

 

[wreckerman893]

I was raised on the old school science fiction of Bradbury, Clark, Heinlein and others of their fame.
My mother was a librarian so I spent a lot of time reading books while I waited for her to get off work.
In our library there were a lot of "anthology" books full of short stories by famous and not so famous writers.
I remember one "Origin of the Species" story to this day.
In it a spaceship from an advanced race lands on earth in the distant past. While the ship was sitting there one of the lazier cooks opened a hatch and dumped a bucket of slop out onto our world. This was against the "Prime Directive" type order that stated that nothing would be left on the planet that could disrupt the natural evolution that would take place here.
In the story one of the ships officers discovers the dereliction of duty after the ship leaves the planet but decides not to return and clean up the mess. He reasons "what's the worse that could happen"?
Bottom line was we all came from leftover alien chow.
And as we all know......the truth is stranger than fiction.