Exploring the Origins of Life

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ribozyme.png Aminoacyl-tRNA synthetase ribozyme, an example of the RNA-based catalysts that may have preceded protein enzymmes during the origin of life.

The Museum of Science at Boston has a fantastic interactive web resource on the origins of life. Exploring Lifes Origins has a timeline of lifes evolution (with sliders), and pages on understanding the RNA world and building protocells, with a nice animation of protocell replication. The pages have been made in collaboration with ribozyme guru Jack Szostak and his laboratory, and there is a handy resources page for educators.

If you are interested in our current understanding of the origin of life, this is a very handy starting off point. You can explore ribozymes in more detail with proteopedia.

(Hat tip to Sandra Porter, biology educators should not miss her blog)

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On The Panda’s Thumb, Ian Musgrave has an interesting entry on the origins of life and the RNA World.  Apropos of this, a nice publication came across my RSS feed late last week.  This study reveals that one of the chemical functionalities that... Read More

37 Comments

If life’s evolution is so well known, why aren’t “scientists” able to create life?

If atomic theroy is so well known, why can’t “physicists” create stars in their basement? (Or recreate the Oklo reactor). Seriously, our understanding of something does not automatically translate into being able to create it (sometimes for simple logistic reasons, tried making a cyclone recently).

That said, our understanding of the origin of life is far from complete (go back and read the linked articles again, then read some of Soztacks articles), but heck, Soztack and Deamer have been making cool protocells recently, so I suppose you can call that creating “life”. (See also this recent article in PNAS (approx 500Kb download).

Hans Mueller Wrote:

If life’s evolution is so well known, why aren’t “scientists” able to create life?

Have you asked that same question to those anti-evolutionists who assert (or increasingly just imply) that life originated many times for all sorts of unrelated lineages? Have you asked them why they don’t even conduct the research to determine or recreate mechanisms of abiogenesis, as “evolutionists” do, even though a theory of abiogenesis is crucial to their “theory,” but not to evolution, which can acommodate abiogenesis being a universe-unique event? One that possibly requires a completely life-free planet to recreate?

Ian Musgrave Wrote:

If atomic theroy is so well known, why can’t “physicists” create stars in their basement?

You haven’t seen me in my basement with my Karaoke machine. Look out Elvis! ;-)

Hans Mueller said:

If life’s evolution is so well known, why aren’t “scientists” able to create life?

You have to much faith in science. The science of abiogenesis (origins of life) is relatively young at less than 100 years, to suggest that in that time scientist would be able to explain and create life from none organic materials is aiming rather high. In the short time we have had science has made tremendous inroads and discoveries have been made.

Perhaps in 100 years we might be able to produce some life, but then again, perhaps not. One thing is for sure in the next 100 years those top notch scientific wiz kids, sure would have cast the torch of enlightenment onto the areas of ignorance. The ride sure will be fun!

Just to piggy back it took 150 after Copernicus for Newton to develop a coherent explanation of planetary motion with the Sun at the “center”, which is a comparatively simpler problem than whipping up a new life form from scratch.

Fellow heathens,

My first online poll:

Why Did God abandon the Republicans in 2008? http://thetimchannel.com/?p=242

Enjoy.

Mr Olaf Wrote:

You have to much faith in science.

With no replies by now, I’m leaning more towards “drive by”.

Hans Mueller said:

If life’s evolution is so well known, why aren’t “scientists” able to create life?

Maybe they have already created life.
It depends on your definition of “life” whether Szostak’s protocells are living or not.

Since life’s evolution is so well known, why do some people refuse to believe it?

DS said:

Since life’s evolution is so well known, why do some people refuse to believe it?

To explain, I quote a robot peasant from the Auto-Hungarian Empire (as featured in Futurama)

“I will believe what I was programed to believe!

Once scientists do create living cells, it will instantly be taken as evidence for the plausibility of intelligent design. There’s an old Latin proverb to the effect that every brick is a weapon in a riot. Religious propagandists go one step farther. For them, everything is a brick.

Hans Mueller said:

If life’s evolution is so well known, why aren’t “scientists” able to create life?

Are you implying that being able to create life in the lab would verify evolution? Are you aware that many evolution deniers argue that creating life in the lab would support ID, since the intelligence of the scientists was required to do so?

Do you agree with them? If so, why did you ask us the question? If not, why aren’t you asking them the question?

Oh, and what’s with the scare quotes around “scientists”? Are you arguing that they aren’t really scientists? If so, what would you suggest we call them?

Ian Musgrave said: Seriously, our understanding of something does not automatically translate into being able to create it (sometimes for simple logistic reasons, tried making a cyclone recently).

I at least am glad that your attempt to make a cyclone failed.

*ducks*

Joshua Zelinsky said:

Ian Musgrave said: Seriously, our understanding of something does not automatically translate into being able to create it (sometimes for simple logistic reasons, tried making a cyclone recently).

I at least am glad that your attempt to make a cyclone failed.

*ducks*

The experiment wound up taking a whirlwind tour of the bathroom sink.

DS Wrote:

Since life’s evolution is so well known, why do some people refuse to believe it?

Lots of reasons. For one it contradicts childhood origins stories. Even when one’s own religion no longer takes the origins stories literally, one often doesn’t know that, or falls for the nonsense that their religious leaders were “bullied” by mainstream science. More importantly, it is wrongly and unfairly portrayed by nearly all anti-evolution activists and many who defend it (especially the clumsy media) as devaluing human life. Add to the mix that most people don’t understand science, can’t grasp geologic time, and love conspiracies, and you have a perfect opportunity for evolution to be the scapegoat in the culture war.

I at least am glad that your attempt to make a cyclone failed.

*ducks*

Yeah, what if that thing had gotten lose, hit a junkyard, and assembled a 747?

Henry

Jim Harrison said:

Once scientists do create living cells, it will instantly be taken as evidence for the plausibility of intelligent design. There’s an old Latin proverb to the effect that every brick is a weapon in a riot. Religious propagandists go one step farther. For them, everything is a brick.

This is a retreat into postmodernism increasingly popular as part of the toolkit of today’s creationists: when denalism becomes increasingly problematic (as in the august assertion that scientists will never create life in a labratory), one simply “interprets” the evidence to mean something utterly counterintuitive, because, according to the deconstructionist theory they pick up in English classes, all we have are subjective impressions of experience, and these competing impressions cannot claim “privilege” over one another. Hence, if I interpret labratory abiogenesis as evidence of intelligent design and you interpret it as decoding the workings of the early earth, it is cultural imperialism for you to “privilege” your impression over mine, since that would demean my experience.

It’s ironic, of course, that religiously conservative American creationists are borrowing tactics from the continental European philosophers in vogue on the academic left, but they both have, for very different reasons, the common agenda of undermining the cultural authority of science, so Michel Foucault and Ken Hamm remain strange bedfellows in the effort to discredit their mutual enemy. (I mean this figuratively, of course, as they would probably not much like talking to one another, especially with the former being dead and all.)

DS said:

Since life’s evolution is so well known, why do some people refuse to believe it?

A variety of reasons. Let me suggest a few First: It is not what people are taught at a young age. I come from a moderate Conservative Jewish family and I learned about the Biblical story of creation before I learned about evolution. This wasn’t an anti-evolution issue or anything like that. But for a 4 or 5 year-old Genesis is easy to explain. So for such people they start with an early perception of an idea other than evolution. Second, the fundamentals of evolution are highly counterintuitive and mind-boggling. You are talking about literally billions of years of time. That’s not a scale humans are used to thinking in. Third, there is the association that evolution is somehow connected to atheism. Forms of that claim are made both by religious individuals and by atheists. So moderately religious people start off with an additional reason not to accept evolution. Fourth, people are not well-educated and are easily swayed by minimally plausible pseudoscience or simple misunderstandings. I was talking to a friend a few days ago in passing made a comment that mutations were always deleterious. This friend is studying to be an engineer at a decent university. But he had almost no biology background. I was able to explain to him what was wrong with the claim but it took some effort. If he were not a smart person or if he had more serious theological reasons behind the claim he likely would have not listened to me. Now multiply that effect by millions of people many of whom do believe there are theological problems and add in a dedicated anti-evolution industry and you get trouble.

The strategies of the apologists are a lot older than “Postmodernism,” whatever that is. Folks in these threads tend to use the word in much the same way that right-wingers use the word “liberal” to refer to anything they don’t like or simply don’t understand. For example, Michel Foucault was hardly a relativist and his line of thought has been continued by extremely serious people such as Ian Hacking, the outstanding historian of statistics.

DS said:

Since life’s evolution is so well known, why do some people refuse to believe it?

Do not overlook the power of childhood training, i.e. indoctrination, bordering on brainwashing.

Children are like vacuum cleaners, they absorb everything that is floating in the air, and it is just their nature to trust and admire parents and teachers.

The result is that at an age when people should be able to think and sort things out for themselves, they are biased beyond repair.

The rest of their lives they are trying to cope. By fighting the theory of evolution to bolster their shaky faith, and to enable themselves and others to believe in the inerrancy and literal truth of the bible.

I wonder what percentage of believers actually are doubters?

Rolf Wrote:

I wonder what percentage of believers actually are doubters?

If you mean what % of those who claim to believe one of the mutually contradictory “literal” interpretations of Genesis privately doubt it, my personal suspicion is that it is much higher than most people think, especially among anti-evolution activists of the “don’t ask, don’t tell” ID variety. Like Ronald Bailey (see the link in my comment of Nov. 9, 5:50 above), I suspect that most activists only pretend to believe a literal Genesis – or refuse to state what they believe in the case of most IDers – in order to keep the “masses” believing their fairy tales, and thus behaving properly.

Furthermore, I suspect that many rank and file creationists who do honestly believe a literal Genesis, believe it in spite of the evidence, not because of it, as professional “scientific” creationists would have them do. One rank and file creationist admitted to me a few years ago that he personally believed a YEC interpretation but conceded that the evidence would not likely support it. Just another of God’s many “tests of faith”, I guess.

JPS said:

…so Michel Foucault and Ken Hamm remain strange bedfellows in the effort to discredit their mutual enemy. (I mean this figuratively, of course, as they would probably not much like talking to one another, especially with the former being dead and all.)

Considering the mindset of the scriptural literalists, I wouldn’t be surprised if Ken Hamm routinely talks to dead people.

Don’t let me interrupt your favorite unsupported anti-religious biases, but you ARE kinda getting away from the thread topic.

FL

FL Wrote:

Don’t let me interrupt your favorite unsupported anti-religious biases, but you ARE kinda getting away from the thread topic.

Thanks. I do need to give due respect to Ian and stop putting off reading the references he so graciously provided. It’s hard to explain to anyone else, but I feel far more in awe of God, and humbled by my own finite physical existence, knowing that my lineage goes back billions of years, not just thousands. But I also feel that much more privileged that God gave me free will so I don’t have to behave like other species just because I’m biologically related to them. I can’t speak for anyone but myself, but for me the senses of humility and privilege tend to keep each other in check.

The result is that at an age when people should be able to think and sort things out for themselves, they are biased beyond repair.

Don’t let me interrupt your favorite unsupported anti-religious biases

QED

Henry J said:

I at least am glad that your attempt to make a cyclone failed.

*ducks*

Yeah, what if that thing had gotten lose, hit a junkyard, and assembled a 747?

Henry

You owe me a new keyboard, sir. This one is now soaked with nasally-launched beverage.

Sorry about that, Chief! :D

Jim Harrison said:

The strategies of the apologists are a lot older than “Postmodernism,” whatever that is. Folks in these threads tend to use the word in much the same way that right-wingers use the word “liberal” to refer to anything they don’t like or simply don’t understand. For example, Michel Foucault was hardly a relativist and his line of thought has been continued by extremely serious people such as Ian Hacking, the outstanding historian of statistics.

Jim,

Since my training is in the humanities and not the sciences, I don’t mean to use postmodernism exclusively as a dirty word, and I use it at all (accepting your suggestion that any definition is vague and that the term itself is frequently a straw man) because “structuralism” and “poststructuralism” are likely not going to be recognized. That said, Foucault’s discursive formations to me closely parallel Kuhn’s paradigms–the idea that truth revolves according to our preferences rather than evolves based upon the accumulation of knowledge, and we only prefer the present version because its ours. And that, as I see it, is quintessentially relativist–the rejection of linearity in order to put all historical ideas about truth and/or knowledge on equal footing.

You only need go as far as Phillip Johnson (or more recently Denyse O’Leary) to get knee-deep in the creationist version of this argument; any interpretation of the evidence is as good as any other, so why not creationism?

I’m hugely oversimplifying, of course, and I’ve wandered horribly off topic, but I’m interested in hearing more about why you feel Foucault cannot be considered relativist.

JPS: I doubt very much if Kuhn would have agreed with you that he was claiming that “truth revolves according to our preferences,” and Foucault, who certainly was interested in how power comports with truth, defended the normal rules of scholarship till his dying day though one can certainly doubt that he lived up to ‘em in his own practice. I think it is an error to put people like Kuhn and Foucault in a narrative about wild-eyed skeptics. I don’t think they were particularly skeptical at all. Trying to understand how scientific ideas come to be and pointing out that their conception was not immaculate is simply not the same thing as denying the validity of the results. I don’t know what you mean by “the rejection of linearity,” but if you mean the rejection of the notion that science works by the repeated application of a cut and dried methodology to facts, I think I reject linearity too, in common not only with Kuhn and Foucault but with almost everybody else since Positivism lost its pop back in the 40s. (By the way, I’m not implying that Positivism is irrelevant because it is out of fashion. I think it’s out of fashion because it turned out to be an inadequate approach to epistemology and the history of science.)

There are some truly absurd people around who know nothing concrete about the sciences–Andrew Ross is the classic case as far as I’m concerned. But then there are always plenty of ridiculous mediocrities around–they are not exactly rare in the hard sciences, either, but nobody bothers to run Sokel hoaxes on those assistant professors. Meanwhile, the philosophy, sociology, and history of science have bloomed over the last fifty years. Why concentrate on the nonentities?

Thanks for posting this.

Maybe the PNAS article (which I have yet to read) hints that Szostak veers away from replicases to be replaced by simpler (say, convective) thermal cycling in heat vents. However that may be that, I assume possible, scenario was treated by cdk007 in one of his excellent videos. The vid neatly complements the ELO material in many ways, especially in regards to evolutionary pathways IMHO. [The actual treatment is the last 7 of 10 minutes, for those who wants to skip the obligatory cretinist debunking.]

Another point mentioned but not elaborated in ELO is that the concentration of fatty acids in heat vents may be too small to allow huge amounts of micelles (at least in open volumes). IIRC last year there were web rumors (news articles, even) of associating production of hydrocarbons (oil) with some heat vents, presumably by isotope analysis. I wonder what become of those rumors, and if true what the detected amounts were.

But what wasn’t mentioned in ELO I think is that AFAIU it has been mentioned that fatty acids can replace prebiotically scarce sugars in nucleosides by way of GNA in a putative pre-RNA world. GNA is said to be thermally stabler than RNA, and presumably the difference affects the cycling scenario in some way in any case. And, not being a chemist, it naively looks to me that the “half sugar” glycerol skeleton is a neat base for evolution to elaborate on as soon as metabolism gets tied into the picture.

Btw, it’s an ageing thread, but I wonder if anybody read this and knows of the “activation” of nucleobases mentioned in ELO; is that the conversion of nucleosides to nucleotides by way of phosphorylation? And in any case, is that activation yet another reaction that is in the montmorillonite’s bags of tricks, or is there other possible prebiotic pathways?

Torbjörn Larsson, OM said:

But what wasn’t mentioned in ELO I think is that AFAIU it has been mentioned that fatty acids can replace prebiotically scarce sugars in nucleosides by way of GNA in a putative pre-RNA world. GNA is said to be thermally stabler than RNA, and presumably the difference affects the cycling scenario in some way in any case. And, not being a chemist, it naively looks to me that the “half sugar” glycerol skeleton is a neat base for evolution to elaborate on as soon as metabolism gets tied into the picture.

GNA also gets you past the chiral issue.

*blinks*
I had to go back and read the full post to remember that ELO stands for “Exploring Life’s Origins” and not the Electric Light Orchestra. Although I’m sure you could find a way to marry the two if you tried really really hard.

Cleanup on aisle 2…

Dunno why this thread slipped from my notes - it was interesting material.

@ Malcolm:

Thanks, I hadn’t considered that. But there was this thread here on PT a while back where chirality was hinted as not being important - seems modern medicine has found that we have ribozymes that converts to and from dangerous or beneficial chiral biomolecules that we can produce or encounter. It may be that observed chirality is a late occurrence, if that was the “issue”.

Protocell Schmotocell

A. “Life from scratch” Relaunching biology from the beginning http://www.sciencenews.org/view/fea[…]from_scratch

B. “Genes’ Expression Modification” http://www.the-scientist.com/commun[…]22.page#3649

Life’s is the ubiquitous cosmic evolution mode. The mode of a gene’s response to the organism culture’s feedback signal, i.e. “replicate without change” or “replicate with change” in case of proven augmented energy constrainment by the offspring, is the mode of Life’s normal evolution, which is the mode of evolution universally, the mode of cosmic evolution.

Dov Henis (Comments From The 22nd Century) 03.2010 Updated Life Manifest http://www.the-scientist.com/commun[…]54.page#5065 Cosmic Evolution Simplified http://www.the-scientist.com/commun[…]22.page#4427 “Gravity Is The Monotheism Of The Cosmos” http://www.the-scientist.com/commun[…]22.page#4887

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This page contains a single entry by Ian Musgrave published on November 8, 2008 9:18 PM.

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