Microbes use arsenic in their DNA: Proves phosphorus is not required for life

http://www.scribd.com/doc/44550217/Science-2010-Wolfe-Simon-Science-1197258

by roadnottaken • 16 years ago

208 127 16 years ago

civilian• 16 years ago

Huh! Biochemistry major here... So I guess that the bacteria just rarely uses Sulphur-Sulphur (thiol) bonds in it's proteins, since Arsenic has a high affinity for it (and that's what causes arsenic toxicity in everything else). http://en.wikipedia.org/wiki/Arsenic#Biochemical_basis_of_ar...

"suggesting the possibility of a biochemistry very different from the one we know" Seems like a bit of an exaggeration, but news will be news. Thiols are important for the structure & enzymatic activity, but this bacteria is proof that there are ways around it. Besides that difference, I'm guessing they're the same.

jaysonelliot2• 16 years ago

You don't think that the discovery of the first organism to use a different element than phosphorous is a big deal?

Cynicism is cool and all that, but this sure sounds like big news to me.

sandipc• 16 years ago

it's a really big deal... provided the arsenic is actually incorporated into nucleic acids, and the bacteria aren't just surviving on background levels of phosphate.

it will be interesting to read the original paper when it comes out in Science later today, and not just accounts of the paper from other sources

dnautics12• 16 years ago

*you don't think the discovery of the first organism to use a different element than sulfur was a big deal?

Oh wait, we all do it.

http://en.wikipedia.org/wiki/Selenocysteine

dotBen2• 16 years ago

it would be a much bigger deal if that element was a replacement for carbon :P

paraschopra• 16 years ago

I'm sure DNA physical structure (angles, bends, etc.) with Arsenic instead of Phosphorous won't be exactly same. Arsenic has same tetrahedral structure as Phosphorous but the atom is sure bigger in size and at DNA scales, size would play a large role in determining shape of molecule. I'm sure you realize that physical interactions play a great role in a cell.

dnautics12• 16 years ago

you would think, but there's also:

http://en.wikipedia.org/wiki/XDNA

It's true that the subtle loss of a hydroxyl group leads to all sorts of differences between RNA and DNA (RNA likes to be single-stranded more than DNA does) but there's TNAs (unfortunate acronyms) and PNAs (not to be confused with PNAS) and other things that basically work and look like DNA with fairly un-subtle changes.

Furthermore, Arsenic really isn't THAT much bigger than Phosphorus (vdw radius 1.85 vs 1.80; covalent radius 1.19 vs 1.06).

crocowhile3• 16 years ago

Yes, beside the fact that they found a way to change the structure of their DNA, RNA, and a few hundreds enzymes involved in energy metabolism they are the same...

This is so huge that my money go into a mistake: I bet these bacteria just found a way to either get rid of arsenic or to neutralize its allosteric toxicity by maskerading or something. The paper is not out yet so I cannot give my opinon on the experimental data but from what I read there is no evidence that DNA actually contains arsenic and until that arrives I believe it's a red herring.

mechanical_fish3• 16 years ago

It does seem overwhelmingly likely to be a mistake. But an exciting one! Biochemistry sports fans like myself will watch with interest.

EDIT: Hey, my upvote voted you down by mistake! Somebody upvote the parent, please.

roadnottaken3• 16 years ago

"from what I read there is no evidence that DNA actually contains arsenic"

FTFA: "When the researchers added radio-labelled arsenate to the solution to track its distribution, they found that arsenic was present in the bacterium's proteins, lipids and metabolites such as ATP and glucose, as well as in the nucleic acids that made up its DNA and RNA. The amounts of arsenate detected were similar to those expected of phosphate in normal cell biochemistry, suggesting that the compound was being used in the same way by the cell.

The team used two different mass-spectrometry techniques to confirm that the bacterium's DNA contained arsenic... Analysis with laser-like X-rays from a synchrotron particle accelerator indicated that this arsenic took the form of arsenate, and made bonds with carbon and oxygen in much the same way as phosphate."

It sounds like there IS some evidence...

colanderman• 16 years ago

Maybe I misread the article but I thought that the bacteria did not multiply if there was neither phosphorous nor arsenic present, but did multiply if there was arsenic but no phosphorous. I could be interpreting this wrong but this seems to rule out "neutralizing" or "getting rid of" the arsenic. (Otherwise why was it unable to multiply in the absence of phosphorous and arsenic?)

jaysonelliot2• 16 years ago

Felisa Wolfe-Simon's name is going to end up in the history books along with Leeuwenhoek and Darwin.

Talk about a life-changing discovery!

spot• 16 years ago

Maybe but not for this work. This wasn't the 2nd origin of life story that was predicted.

mechanical_fish3• 16 years ago

Yes, the touchstone of everyone's work should be how well it compares to the figments of one's imagination.

Poor Einstein! If only he'd discovered warp drive, he'd be as famous as Zephraim Cochrane!

frisco4• 16 years ago

This seems silly. Phosphorous not being required for life seems obvious to me: ok, maybe it's believed to be used in all Earth-originated, carbon-based life, but why would we believe a priori that it's an absolutely necessary component of any biological life anywhere (which seems to be what's implied by NASA and the relation of this to exobiology)? If we develop silicon-based artificial intelligence (how do you define life, anyway? That matters when you're talking about astrobiology), would we run a headline, "Researchers prove carbon not required for life"?

I've always thought the scientific community stated that alien life may use a totally different biochemistry from us?

Edit: so, in some senses this is like P!=NP being proven, except less important, since it's only one component (phosphorus). It's scientifically a big deal but doesn't change the world because it's largely what we've always expected (the metaphor breaks down that this doesn't have the major secondary consequences like N=NP would).

davidsiems• 16 years ago

http://lesswrong.com/lw/im/hindsight_devalues_science/

frisco4• 16 years ago

I don't think this is hindsight bias though. As a scientist (not in biochemistry or astrobiology, though) I understand this had to be specifically shown, but this is one of those things that most people I talk to and I have always just casually treated as obvious. The confirmation is important scientifically, but shouldn't change our viewpoint, since it's what we've always expected. Am I wrong here? Any computational biologists or biochemists want to tell me this wasn't expected at all?

flogic2• 16 years ago

Speaking without any domain knowledge, I think it has to do with "what can support the complexity required for life?". I would think it requires molecules that can do interesting things while at the same time survive their environment long enough to do those things.

frisco4• 16 years ago

It has to do with electronegativity and number of free electrons. Both phosphorous and arsenic can make three bonds, and arsenic is only very slightly less electronegative than phosphorous.

bad_user• 16 years ago

> Phosphorous not being required for life seems obvious to me

It hasn't been noticed or proved, and conclusions drawn from actual science have a tendency to disprove common sense once in a while, which makes any actual discovery worthwhile.

InclinedPlane3• 16 years ago

Obvious, yes (which is why people have been looking for examples). Proven, no, not until now. That's why this is important.

archgoon• 16 years ago

Suppose Monopoles were discovered. Nothing really rules out their existence, Gauss's Law for magnetism is just an assertion that we've never seen a monopole, it's possible to patch up maxwell's equations to get monopoles. To some people, the existence of monopoles is 'obvious'.

It would still be a very big deal if monopoles were to be discovered, even in trace amounts, and no feasible way to make more of them.

sorbus• 16 years ago

"The researchers isolated the organism and found that when cultured in arsenate solution it grew 60% as fast as it did in phosphate solution — not as well, but still robustly. The culture did not grow at all when deprived of both arsenate and phosphate."

akharris2• 16 years ago

Two weeks ago: antimatter contained long enough to be studied.

This week: life without phosphorous.

Next week: flying skateboards?

cryptoz5• 16 years ago

I think the first artificial, human directed production of antimatter was by CERN in 1995. I'm not sure what you mean by "two weeks ago", but antimatter has been around a lot longer than that.

akharris2• 16 years ago

Two weeks ago, CERN made the announcement that they had contained antimatter long enough (at LHC) to study it properly. First time it's ever been done that well. Pretty stunning accomplishment.

prawn• 16 years ago

On flying skateboards, we were wondering the other day in the office about Parrot-style drones that you could hang from:

http://www.blogcdn.com/www.engadget.com/media/2010/01/parrot...

Risky, but I'd try it!

TheSOB883• 16 years ago

Why people constantly stick to the idea that all possible organisms must have similar biochemistry to us is beyond me.

Think about it: Out of the humongous search space of chemicals, the ones we use happened to work for us. A combination of randomness and building on what worked before got us to where we are. Why should life not be able to use chemistry in completely different ways in order to replicate itself? Why are we so arrogant as to think that our design is the only design?

Edit: My point is that our ratio of "shit we know" to "shit we don't know we don't know" is infinitesimally small in the field of possible lifeforms' biochemistry. That is, we only know stuff very close to us on a cosmic scale; we effectively have blinders to all other possibilities. And there's already a lot of biochemical variation on Earth: To give some small examples, viruses don't even have DNA, and plants use less amino acids than animals.

The self-similarity of what we have so far can be explained, I think, by evolution. We all started out from the same point, so there's very little incentive to "reinvent the wheel" as it were. Only under extreme conditions like we have here, or the geothermal vents underwater, do we observe marked differences.

cryptoz5• 16 years ago

> Why are we so arrogant as to think that our design is the only design?

We're not. Nobody is. The reason scientists don't look for life on other planets that is made of other chemicals is that we may not be able to recognize that as life. It's much better - read, scientific - to look for something we can recognize.

Also, there are chemical properties of the elements that make up life on Earth that allow for fast reactions, bonding, etc. Most of the rest of the elements in the periodic table react more slowly in normal conditions, making the process for life less likely. Not impossible. Just less likely. We think.

So we focus on looking for what we know about. That's the best way to do it. Nobody worth their degree will ever claim that our "design" (bad word choice, by the way) is the only one.

TheSOB883• 16 years ago

I wasn't trying to address any bearing this has on finding alien life, just speaking theoretically - we shouldn't assume that everything should be like us. If it hasn't been your experience that most people think that way, then I must have misjudged.

I agree on the second paragraph, but especially the last sentence.

I know "design" is used by IDers, but what other word can adequately reference the incredibly complicated way our cells and bodies work?

Thanks for the response.

joe_the_user• 16 years ago

I agree with you that other life structures seem quite possible. I don't see the problem. But I'm not a professional biologists.

Still, it seems there are a number of biochemists who believe (or believed) that the structure of earth life could be unique. These people knew a lot more than me. So I wouldn't credit this to arrogance so much as a very complex question, one that doesn't necessarily get easier to solve the most data you get (at least on our scale of data).

rhizome• 16 years ago

I don't think it explictly comes down to such hubris. Certainly there are a lot of biases in this subject just like there are in any other ("rap isn't music," for instance), and human history is rife with analyzing the world in terms of the analyzer's perspective, the very definition of bias.

While replacing nitrogen in the air with, oh, sulfur, would likely have resulted in life forms (so the story goes) with an entirely different chain of evolutionary reactions and mutations, resulting in different body chemistry, yadda yadda yadda.

I do think it's news when we find out what one of these parallel evolutions might consist of. I mean, I'm not even sure sulfur-air would be a gas, so it's one thing to guess and speculate (fun), it's quite another to be able to say, in scientific fashion, "OK, what else is possible on this arsenic branch?" Said another way: there are a lot of grant proposals being written right now to finance exploration of this new territory. Hey, it beats paying for research into animals who produce petrochemicals as blood.

benatkin• 16 years ago

I think you might have confused unwillingness to talk about things we don't know with unwillingness to admit the possibility of things we don't know. Having some knowledge in common helps make conversations interesting. When two people talk about a possibility that's in the head of one of the participants, the conversation is unlikely to be on equal footing.

ugh2• 16 years ago

Who are people in this case? Most people don’t at all know what kind of life is plausible and not and they don’t care. I’m certain, however, that many biologists had an opinion on this prior to the discovery and I’m not really sure whether they thought that it was unlikely. For all we know most biologists expected this or a similar discovery, they just couldn’t yet assume it to be true because there wasn’t any evidence. Until now.

dnautics12• 16 years ago

I don't know. You would think, but you can autoclave a solution of "deionized ultrafiltered water" which should have "no" carbon in it at all, and bacteria will find a way to grow in it if you get it contaminated, they will concentrate the trace trace trace amounts of carbon.

How carefully did they prep their DNA? These days nobody is careful and they use these crap kits which are good enough, convenient enough to get molecular biology done. The other day in lab I suggested someone isolate DNA using caesium chloride gradient ultracentifugation and the only people who knew what I was talking about were the two old (70+) year old senior scientists but they agreed that it was the way to go.

drcode• 16 years ago

OK, this news is very interesting, but it does not prove much about extraterrestrial life.

We know that organisms can adapt to their environment. Incorporating some fraction of arsenic into a cell's dna is an example of such adaptation.

The question that really matters is "has life originated more than once in the universe?" This experiment has no bearing on that: They took a standard terrestrial cell, with a carbon-based history, and simply subjected it to some new conditions. This is NOT a new life form that originated from a novel environment and using a different chemistry. However, NASA is getting awfully close to selling it as such in their press conference, which is misleading.

jpwagner4• 16 years ago

I think this finding deserves a bit more respect.

Of course it does not answer ALL of our questions, but it proves DNA does not need phosphorus! AMAZING!

Archaeum3• 16 years ago

I agree that this is remarkable, but I think it's valid to criticize publicizing the finding as an astrobiology discovery, which is exactly what NASA (or its public relations department, at any rate) is calling it--and which it is not, despite its implications for astrobiology.

If we care about engaging the public, we should be concerned about sensationalism that detracts from the solid work of the scientists. If you cause people to think you're going to show them extraterrestrial life, fairly or not, you run the risk of them tuning out when the reality is less flashy, even if it's groundbreaking.

dnautics12• 16 years ago

So, exactly where in the paper did they show that there was DNA that had an arsenic backbone? They just showed that there was arsenic in the sample that they think is DNA, and not very much phosphorus. That could be contaminants. But also, how do they know that sample is the "DNA sample"?

noodle3• 16 years ago

if you're watching the press conference, they're very adamant that it doesn't prove anything about extraterrestrial life and they aren't able to yet say if life evolved with the arsenic or if it adapted.

but they're pointing out that it does show that forms of life different from our current definitions can exist and therefore the possibility of extraterrestrial life in non-earthlike environments exist.

albertzeyer• 16 years ago

I'm not a biologist but:

Assuming that arsenic life just adapted, we don't know if it is possible that arsenic life can evolve in a non-earthlike environment or not, do we?

I.e. we don't know if life can evolve in a non-earthlike environment.

jerf4• 16 years ago

"but they're pointing out that it does show that forms of life different from our current definitions can exist"

Yes, but not meaningfully different from previous definitions. If this is simply an evolution of existing earth life, then it's just another in a long list of things that we were surprised evolved from conventional Earth life, but is, nevertheless, conventional Earth life. It's more indicative of a slight flaw in our definitions, not time for a radical reexamination of our assessment of the universe.

As I commented in a previous message, people have a history of getting far more excited about this sort of thing than they have scientific justification for. This sure looks like another one of those.

Now, if they could establish that this has to be the actual entirely new branch of life that can be provably not traced back to the same Earth ancestor as everything else, that would be a groundshaking discovery.

Those of us pondering the Great Questions were already not assuming that everything has to look exactly like known Earth life to work. There are numerous obvious different, incompatible mechanism that could exist (different RNA transcription tables, the other chirality for proteins) and an unknown and presumably vastly larger number of unobvious different mechanisms even just for basically Earth life before we really go out into new territory. We've already speculated endlessly about silicon life, ammonia life, mechanisms other than photosynthesis, etc. Don't get me wrong, this is legitimately interesting, and would on its own be worthy of HN, but I have to say the implications for the Great Questions are basically zip. Announcing proof that life can only exist in precisely Earthlike conditions with incredibly tight tolerances would be the surprise.

bradfordw• 16 years ago

It has its own twitter account! https://twitter.com/#!/ArsenicBacteria

cryptoz5• 16 years ago

s/it's/its

cstross2• 16 years ago

As Mono Lake is of volcanic origin and formed around 760,000 years ago (per Wikipedia) I'd be astonished if the arsenophile(?) evolved there in that short a time span. Which leaves open the question of where it came from, and whether arsenic tolerance is present but dormant in other extremophiles.

Other points of note: never mind the cellular DNA integrating arsenate, the whole respiration cycle seems to be affected, presumably running on ATA rather than ATP. Which implies huge amounts of molecular booty in the shape of enzymes that are powered by a different reduction gradient (ATA-AMA rather than ATP-AMP).

Possible down to earth applications? Lest we forget, Pakistan has a monstrous problem with arsenic-contaminated wells ( http://www.irc.nl/page/16331 ) and a bacterial culture that thrives on arsenic could offer new approaches to arsenic sequestration. And that's just off the top of my head. (My biochemistry is, alas, too rusty to go much further without a refresher course. Hmm ...)

jacquesm2• 16 years ago

If a bacterium consumes the arsenic from a contaminated well the well is now contaminated with the corpses of bacteria that are rich in arsenic.

You'd have to add another pass to get rid of the bacterial residue (possibly easier, but still).

enjo• 16 years ago

Doesn't that depend on the byproduct produced by the respiration cycle?

sudont• 16 years ago

Possibly a small sludge pond that would filter the water through as per a sewage treatment plant?

I'm thinking that if it's in the wells, it's due to the solvent action of water on the rocks, and cleaning out the wells would only be a temporary solution.

lukeschlather• 16 years ago

Clearly, the bacteria aren't going to magically destroy the arsenic. But eat the arsenic, die and float to the surface of the well where they can be skimmed off? I'd say that's a simple goal for some genetic engineers to start gunning for.

It's also plausible they could metabolize it into some non-toxic form. (We've got a variety of biomolecules we've never seen before, some of which could be non-toxic.)

InclinedPlane3• 16 years ago

Arsenic is this big: (makes gesture with thumb and forefinger a few angstroms apart), bacteria are this big: (makes gesture with thumb and forefinger a few microns apart).

OK, that's not overly helpful, the point being, you can filter bacteria out of water a whole hell of a lot easier than you can filter out dissolved arsenic.

dotBen2• 16 years ago

Back in the discussion thread pre-announcement a few days back, I mentioned Mono Lake as potentially being a source for this (http://news.ycombinator.com/item?id=1953749 and http://news.ycombinator.com/item?id=1953756).

I just wanted to reiterate my suggestion for any bio-geeks living in the Bay Area - Mono Lake is only 2hrs drive from Bay Area and it is FASCINATING.

I would really encourage anyone who is interested in ecology and biochemistry to go check it out if you are passing through to Mammouth Lakes for snowboarding or taking a trip to Yosemite which is next door.

hyperbovine• 16 years ago

Do you have any basis for the claim the 760k years would not be enough time for such a feature to arise? After all, some surprisingly complicated things (http://en.wikipedia.org/wiki/Evolution_of_the_eye) are believed to have evolved (more than once) over shorter periods.

philwelch2• 16 years ago

Number of years is mathematically irrelevant. Number of generations is mathematically relevant. Bacteria produce new generations prodigiously.

Consider: antibiotics were invented less than a century ago, and bacteria have already evolved a resistance to penicillin. That's probably more than humans have evolved for 100,000 years. 100 years is like five generations for humans, but billions of generations for a bacteria. 760,000 years? That's tons of time for bacteria. Especially since bacteria are pretty simple; more complicated life has a much harder time evolving.

dnautics12• 16 years ago

"I'd be astonished if the arsenophile(?) evolved there in that short a time span"

Why not?

http://en.wikipedia.org/wiki/Berkeley_Pit#Extremophiles

BTW, the ATP-AMP reaction is not a electrochemical reduction reaction, it's rather the mundane hydrolysis of a phosphodiester bond. We don't know what the energy potential of an arsenodiester bond is (although some speculation is that it carries a bit less energy).

cKeyser• 16 years ago

I'd use the word arsenotolerant instead. The cells still preferentially utilize phosphorous when given the option. The prefix phile generally implies that they require such conditions to live, like a thermophile isn't viable at a temperature below (roughly) 40 C. This organism would have no trouble growing in the absence of Arsenic. =)

roadnottaken3• 16 years ago

Here's the article from Science: http://www.scribd.com/doc/44550217/Science-2010-Wolfe-Simon-...

stavrianos• 16 years ago

bicycle discovered constructed entirely from wood: proves metal not required for transportation

http://www.leevalley.com/newsletters/woodworking/2/3/article...

anigbrowl2• 16 years ago

We already knew that because we have had wooden boats, carts, and planes (gliders).

jjs• 16 years ago

You're missing the point—this is the single greatest discovery in exobicyclology since E.T.!

bld• 16 years ago

Here's the press conference in three ~10 minute parts: Part 1: http://www.youtube.com/watch?v=hu5dXnCUs7I Part 2: http://www.youtube.com/watch?v=0LsihAsX4z8 Part 3: http://www.youtube.com/watch?v=Nu0VvxuicLw

The lead author gives a talk at 2:26 in Part 1 that I thought was an excellent example of how to communicate science (or other technical subject) and implications to a general audience.

olalonde2• 16 years ago

Most theories[1] agree to say that replicating life predates DNA. Wouldn't that mean that we could still have a common ancestor with this life form?

[1] http://en.wikipedia.org/wiki/Abiogenesis#Other_models

joelburget5• 16 years ago

We not only could have a common ancestor, it seems to me to be almost certain. What are the chances that some other life has evolved with DNA completely independently

olalonde2• 16 years ago

I second, but that's what the first article posted on HN seemed to suggest. http://skymania.com/wp/2010/11/alien-life-form-is-here-on-ea...

yread• 16 years ago

Why do you consider it certain? It could have just died off being much less efficient than us.

joelburget5• 16 years ago

Perhaps NASA should be more cautious about holding a press on astrobiology, and with a Science embargo. Clearly everyone will immediately think of aliens, and for good reason. It's NASA, it's about astrobiology, and it's something big enough to embargo Science. They're just asking for all the alien stories. And let's be clear, these are not aliens.

ugh2• 16 years ago

Holding a press conference for this pretty sweet discovery was completely justified. The language in the press release made it clear ahead of time that Nasa didn’t make any discovery related to life on other worlds, only a few overly eager bloggers spun crazy theories like that.

Whoever is disappointed by this and claims that Nasa hyped too much doesn’t have her or his head screwed on right.

joelburget5• 16 years ago

I agree that it's an amazing discovery. Admittedly I didn't read the actual press release so you're probably right that they acted correctly. I only read second hand accounts of what they were going to announce.

dnautics12• 16 years ago

high resolution Mass spec is such a shitty technique and is completely non-quantitative. How do you know that arsenic isn't associated with, say, a protein that makes the DNA resistant to being taken apart chemically. I will believe this result when they stain the DNA and run samples of the DNA down a density gradient ultracentrifugation and show that arsenic content in the media correlates with increased density of DNA, as you would expect if the arsenic is replacing phosphorus. If you don't know what i'm talking about, it's this classical experiment:

http://en.wikipedia.org/wiki/Semiconservative_replication#Bi...

Here is my personal scientific experience speaking: If you see it everywhere, then it's likely to be an artefact. Clean up your technique, clean your instruments, and go back to an old school technique. Remember how the physicists who discovered CMB cleaned out the pigeon scat from their microwave horn telescope before they started to believe what they saw.

EGreg7• 16 years ago

Don't mean to get all religious on ya, but I wanted to ask here...

Is there any evidence of macro-evolution having ever taken place in recorded history? I'm asking this with no agenda, but curious. As far as I know, no new species have ever been produced, despite natural or unnatural selection.

So what makes us say that there is no other force or process that causes speciation? How are scientists so convinced that mutation and natural selection is all that is required, despite never having observed a single instance of speciation?

To be scientific, a theory has to make some potentially falsifiable, non-obvious predictions. Then we can test those predictions, and if our experiments confirm them then the theory survives. I totally agree that the hypothesis "natural selection occurs" has been proven in ample ways (ok, maybe the white->dark->white butterflies was a bad one, but bacteria and their resistance to antibiotics is proof enough). But to form a completely new species...

Species is defined as "as a group of organisms capable of interbreeding and producing fertile offspring" according to Wikipedia. Two animals are of different species if none of their offspring have ever been observed to be fertile. At least, that's a good working definition.

It bothers me that scientists have been interbreeding literally thousands of generations of fruit flies and despite all selection pressures, artificial or not, were never able to produce a single new species. Sure, it's hard to try and mate every fruit fly with every other fruit fly, so maybe there were divergent species, but after a few generations, this should have revealed itself. If this is really the case, then how come we take it for granted that humans, homo erectus, neanderthals etc. were all divergent species that had a common ancestor something like 50,000 years ago? Am I way off? If you take the fruit fly lifetimes and human lifetimes, in those 50,000 years we had about as many generations as the fruit fly generations. And we got all this speciation supposedly, using nothing more than mutation and natural selection. But where is the proof?

I'm not necessary arguing that one of the religions is right and there is another force. But are scientists being biased here when they simply assume there isn't any other force? It's as if I was looking at cars from the 1920s all the way up until now, and I saw gradual change, and based on this I decided that there was no designer of these cars. I don't think that follows at all.

Just curious if someone knows links that can resolve this for me :)

dnautics12• 16 years ago

http://en.wikipedia.org/wiki/E._coli_long-term_evolution_exp...

jerf4• 16 years ago

http://www.talkorigins.org/faqs/comdesc/

baxter2• 16 years ago

With no description I almost didn't click on this link, but I'm glad that I did. The title of the paper it links to is "29+ Evidences for Macroevolution, The Scientific Case for Common Descent" and is worth a look.

EGreg7• 16 years ago

Yes, I have seen talkorigins before and I use this all the time when people ask "how do you prove macroevolution"?

Certainly I can prove that macroevolution has taken place, if by that you mean that natural selection and mutation take place, and that the change is gradual, and topologically continuous.

"A unique, historical phylogenic tree" -- this pretty much expresses that idea.

But where in that paper does it talk about actual testable predictions of the hypothesis: "all speciation came about as a result of mutation and natural selection with no other factors or forces"?

Each section has a "predictions" section. But notice that even if all these predictions come true 100% of the time, this does not rule out the possibility that new species of sexually reproducing organisms are created specially by God, much like new cars are created by humans, despite there being an observably continuous change through time.

http://www.talkorigins.org/faqs/comdesc/section5.html#specia...

Look at this. We are almost there, to what I am looking for. Are these "speciation events" fitting the "mating preference" criteria or "cannot produce fertile offspring" criteria? If the latter, I am satisfied!

npad• 16 years ago

http://en.wikipedia.org/wiki/Speciation#Artificial_speciatio...

dnautics12• 16 years ago

It's supposedly an industrial secret, but hearsay is that Abbott laboratories took the strain of bacteria that makes erythromycin and began serial UV-mutagenesis it to improve titers. It went from trace production to making 10-50 grams of drug per liter of media, which is quite amazing. As a result the bacteria has reconfigured its entire metabolism. Started out as a sessile, filamentous bacteria with a highly complex life cycle and now is a roughly spherical free-floating bacteria.

"Species is defined as "as a group of organisms capable of interbreeding and producing fertile offspring" according to Wikipedia. Two animals are of different species if none of their offspring have ever been observed to be fertile. At least, that's a good working definition."

Just so you know: That is just about the worst definition for microbiologist. Bacteria don't grow by sexual reproduction, they reproduce by binary fission. They also share genes like crazy. I've seen a gene taken from a sargasso sea sample crop up in the database for a bacterium found in the deeps of the medeterranean ocean. There is speculation that a virus is responsible for spreading photosynthesis between several different, otherwise very distantly-related clades of bacteria.

EGreg7• 16 years ago

Yes, but look at what you are saying.

I fully agree that bacteria, rotifers, and other creatures can pick up genes. This is incredible. In fact, they've just found bacteria that substitute entire elements, which is incredible too.

What I am asking about, is the specific hypothesis:

"all speciation occurred via repeated application of mutation and natural selection, and no other factors were involved"

Now, I realize this would be impossible to test for ALL species, but wouldn't it be nice to have an example of at least ONE species that arose in this way through sexual reproduction? We have been breeding dogs for hundreds and thousands of years, and all of them are the same species! We have been adapting plants and never been able to create new species. Why is it so hard to do it, or it's just that we haven't tried hard enough?

I'm basically taking a skeptical approach here to the hypothesis, you see what I mean? It would be nice to just call it all "evolution" and assume the results. But I'd like some proof, some falsifiable predictions that have been tested.

baxter2• 16 years ago

I was under the impression that artificial speciation had been achieved. Have I misunderstood http://en.wikipedia.org/wiki/Speciation#Artificial_speciatio...?

EGreg7• 16 years ago

I just looked at that section. They present three examples:

flies - but they say only a "mating preference" was achieved. Well sure, there are different kinds of dogs and they probably prefer their own kind, but they are still just one species.

domestic cattle - this is a non-example, as the article points out, because they are all capable of interbreeding

sheep - two kinds of sheep are apparently different species. However, I would take issue with this statement: "For example, domestic sheep were created by hybridisation"... it seems inconsistent with the other one: "but the initial dates and methods of the initiation of such species are not clear". How do they know they were created by hybridisation?

icegreentea• 16 years ago

It depends exactly how strictly you define speciation. If you follow the 'weak' version of 'these two populations will not normally breed with each other and create viable offspring' then we've done it a few times with flies [1]. We've created populations that will not normally breed with each other.

If you pick a stronger version, where they -cannot- breed, even if you were to preform in vitro or something similar on them, then we haven't quite done that yet.

[1] http://www.jstor.org/pss/2410209 (overview of attempts to record speciation in a lab)

EGreg7• 16 years ago

interesting paper!

gort3• 16 years ago

"How are scientists so convinced that mutation and natural selection is all that is required"

They believe no such thing. Selection isn't required for allopatric speciation. Two isolated populations will naturally start to diverge just due to drift (random genetic changes over time). Given enough time they will inevitably become sexually incompatible.

"As far as I know, no new species have ever been produced, despite natural or unnatural selection."

Then let me direct you to: http://tinyurl.com/ridley2004speciation

"We begin with two distinct, but related species. The pollen of one is painted on the stigma of the other. If a hybrid offspring is generated, it is usually sterile ... However ... the chemical colchicine can often restore hybrid fertility. It does so by causing the hybrid to double its number of chromosomes ... Hybrids so produced may be interfertile with other hybrids like themselves, but not with the parental species. They are then a new reproductive species."

"Most garden varieties of irises, tulips, and dahlias, for example, are artificially created species. But their numbers are dwarfed by the huge numbers of artificial hybrid species of orchids, which it has been estimated are being formed at the rate of about 300 per month."

"Polyploid hybridization is also important in natural plant evolution."

Now, that type of speciation is a special case. It is not how animals speciate. But you are quite wrong in your quoted statement above.

"how come we take it for granted that humans, homo erectus, neanderthals etc. were all divergent species that had a common ancestor something like 50,000 years ago? Am I way off?"

Yes, you are, by an order of magnitude. Homo neanderthalensis is supposed to have diverged 500,000 - 800,000 years ago. http://dx.doi.org/10.1126/science.316.5827.967a ("The new findings also push back the date that Neandertals split from the human branch of the primate tree by 200,000 years—to 800,000 years ago")

"maybe the white->dark->white butterflies was a bad one"

Don't believe everything you read in AnswersInGenesis. This is still a good example. Or at least, so I believe on the basis of http://bostonreview.net/BR35.2/block_kitcher.php - "These are interesting alternatives to the familiar story, and the causal hypotheses they introduce can be tested in obvious ways: by examining the rates of larvae survival or by investigating nocturnal motions of moths. And this is what biologists have done."

But I don't have time to dig into the primary literature.

"scientists have been interbreeding literally thousands of generations of fruit flies and despite all selection pressures, artificial or not, were never able to produce a single new species"

Do you have examples where this has been the actual goal? I know Dodd (1989, http://eebweb.arizona.edu/courses/ecol525/readings/dodd_1989... ) tried this, but I don't think the experiment ran that long.

You will appreciate that it is much more effort for me to correct your poorly-informed naysaying than it is for you to naysay.

EGreg7• 16 years ago

Thanks, man. Now I have some good resources to refer to when people doubt speciation or macroevolution.

Although this doesn't prove that all species came about through mutation and natural selection only, it does give examples of this happening. I didn't know it happened in plants.

And thanks for setting the record straight on what people believe regarding our common ancestor with neanderthals. Offhand, I thought it was a mere 50k years :P Are there any hominids that split from us more recently? Like 50k?

gort3• 16 years ago

If you have access (i.e. from university or whatnot) the actual paper is now online at:

http://www.sciencemag.org/content/early/2010/12/01/science.1...

vibragiel• 16 years ago

"It's not arsenic-based life"

http://scienceblogs.com/pharyngula/2010/12/its_not_an_arseni...

Microbes use arsenic in their DNA: Proves phosphorus is not required for life

Related Stories