ResearchBlogging.orgIn his highly readable book, One Long Argument, Ernst Mayr breaks down the body of thought often referred to as “Darwin’s Theory” into five separate and distinct theories, the second of which being “common descent.” Darwin’s second evolutionary theory (second by Mayr’s count, not Darwin’s) is really a hypothesis that could be worded this way:

All life on earth descended from a single, original, primordial form that arose eons ago.

The evidence in favor of this hypothesis is strong, but the test of the hypothesis … the means of disproving it, which is, after all, the point of stating it to begin with … is difficult to define, but like pornography to a judge, one would know it when one sees it.

The question at hand is, does the current finding reported moments ago by NASA relate to this concept at all? The answer, as you’ll see, is yes. And no.

The evidence for a single origin is this: There are a lot of potential variations in how life works, but only a very small and rather quirky subset of those variations exists in every known organism on this planet, strongly suggesting a single origin which left, as a sort of timeless imprint, that selectivity and quirkiness. Hundreds of amino acids are known to exist, but only 20 are used as the basic building blocks of life. The genetic code (the codons that specify those building blocks) is odd and quirky, but exists with very little variation across all lifeforms. Certain complex molecules, most notably the ribosomes that are key in forming complex molecules such as proteins on the basis of the genetic code, are large, clunky, and made up of sequences that could easily be very different than they are and still work, but nonetheless follow a very limited pattern, strongly suggesting that all existing forms have but one ancestor. DNA itself is pretty much the same everywhere, suggesting, again, a single origin.

If life arose on Earth more than once, there would likely be more than one quirky, finger-print like pattern of coding, building blocks, and complex molecules. And there isn’t. Right?

Well, if you’ve read my blog long enough, you probably know that I would not have explained all of this if there was not some way to turn around and explain how it’s all wrong.

First, we have the latest news from NASA. It turns out that there is a form of life that is different, in a very fundamental way, from all other life forms on the planet. It is a bacteria-like form that appears to be able to use arsenic instead of phosphorous in forming its DNA, and probably in other functions as well, known by the term “strain GFAJ-1 of the Halomonadaceae” (hereafter referred to as “the bacterium”). Given the model I’ve just described, this is a potential falsification of the Darwinian hypothesis that life originated once.

Now, before we go all “Darwin-was-wrong!!!11!!” on this, let me be very clear: This hypothesis … that all life has a single origin … is singularly unimportant to overall Darwinian or Evolutionary theory. If, indeed, life originated different times and different places so that today there were different environments (or continents, or whatever) with diversified forms of each separate origin, that may have been noticed by Darwin (or later biologists) and the multi-origin would simply be a fact. If each set of life types had diversified into different species and otherwise been very Darwiny in history and behavior, with Natural Selection working in all the distinct lineages, etc., the other four of Darwin’s theories (as told by Mayr) would be very strongly supported, because Darwinian processes would be seen to play out in multiple instances. Similarly, if we find that life started up at different times and different places elsewhere in the universe (on other planets) then this would address similar questions. Who knows? There may even be non-Darwinian life forms that arose in a certain pattern and never changed thereafter. Darwinian evolution requires that imperfect copies are made each generation. A life form that copies itself perfectly, or one in which imperfection always leads to termination of a lineage, would never posses the variation that Natural Selection works on. You can see why the discovery of extra-terrestrial lifeforms would be very interesting to biologists!

But I digress, somewhat. What we have now is a proposal that all life on Earth has the same origin because all known forms have the same somewhat to very quirky variants in how they work that act as an individual, unique fingerprint pointing to one origin. The Mono Lake find, however, is an organism with at least one aspect of that quirky how-life-works pattern that is different. Does this falsify the Darwinian hypothesis?

The Mono lake life form is a bacterium. A team of scientists started with a culture of bacteria from Mono lake, an utterly inhospitable environment in California (near Nevada, east of the Bay Area) in which life seems to thrive against the odds. This was placed in a medium that contained all the necessities of bacterial life, to allow the bacteria to be alive, to thrive, to grow, and to reproduce, except phosphorus. This soup also contained a high level of arsenic.

They did this because the lead scientist on the team, the Carl Sagan-like Felisa Wolfe-Simon, was considering the preposterous idea that arsenic could substitute for Phosphorus in some biological systems. There were no known cases where that actually happened, but arsenic does in fact replace phosphorus very easily, which is why it is a poison for many organisms. If you put together the elements that make up key organic molecules in a test tube and shake it, usually nothing happens unless there is a set of other molecules (enzymes) and some ATP and stuff to make it assemble as it should. But if you put arsenic instead of phosphorus in the same soup, you get at least partial reactions that look like the formation of organic structures. In other words, given an atom of arsenic and an atom of phosphorus, the arsenic had a better chance of insinuating itself into certain key positions than the phosphorus element. Also, arsenic is more reactive than phosphorus.

Here’s the thing: Phosphorus is often used in molecules in places where it provides important stability, once it is in place. It forms the very backbone that keeps the DNA molecule together. If arsenic, chemically similar to phosphorus but more reactive, is accidentally substituted, the stability is compromised. Arsenic is such an effective poison for this very reason. It’s like a suicide bomber dressed like a security agent. It easily gets into an important location, then it ‘reacts’ with stuff and messes everything up.

But owing to some sort of brilliant insight, Wolf-Simon thought arsenic could sometimes substitute for Phosphorus, and she reasoned that the best place to find that biological difference would be in organisms that had evolved in a place where there was a LOT of arsenic, yet life still existed despite the presence of this nominal poison.

Thus the experiment. And it worked. Even in the absence of phosphorous, in an arsenic rich environment, a bacterium thrived. (This is an oversimplification, but that is the general idea.) When they looked more closely, they discovered that the arsenic had substituted for phosphorus in part of the DNA of the bacterium.

Now, consider for a moment (but no longer than a moment) a life form that uses arsenic instead of phosphorous. As the backbone of the DNA, as part of the energy-system molecules of ATP, and elsewhere, arsenic is used instead of phosphorous. That would be a life form that had a quirk that was distinctly different from the usual finger-print like quirks that generally convince us that all life has a single origin. It might be an organisms that evolved from a separate origin.

Is that the case here?

No, I don’t think so, but there are two ways in which this finding can inform and guide research into the possibility of multiple origins of life on earth.

It has not yet been demonstrated that arsenic substitutes for phosphorus in all reactions in these bacteria. The bacteria could have had some of their own phosphorus, and only most but not all was substituted. It also seems that this organism uses arsenic in a facilitative rather than obligatorily manner. In other words, this bacterium uses phosphorus in the usual way, but can substitute arsenic under certain conditions. Also, it has not been demonstrated that the other quirky bits of the inner workings of the cell are different from the norm in this organism. So, it would appear that this is a bacterium that has secondarily evolved a trait, viable substitution of arsenic for phosphorus, and not a separate lineage.

There are two (really, three) ways that this finding could speak to Darwin’s second theory.

One is that the above is wrong … that it will be discovered that this “bacterium” has a different ribosome, and other differences, and really is a different form of life that originated separately from the rest of life on earth, but has not been investigated closely enough yet to know these things. My reading of the paper and observation of today’s press conference at NASA makes me think not, so let’s leave that one aside. Maybe we’ll be shocked later on this issue, but I think not.

So, the other two ways in which this finding relates to Darwin’s second theory are 1) This could suggest a high diversity of life forms early in life, which could mean that the origin is not a point so much as a committee of diverse experiments that finally settled on the current system of double-helix phosphorus-spined DNA, RNAs, ribosomes, and so one and 2) By demonstrating that an entire life system could use arsenic and not use phosphorus at all.

The first of these may be a bit esoteric, but nonetheless interesting. What I’m suggesting here is that the origin of life involved several different biochemical experiments that would now and then spatially overlap, and when they did so, sometimes combined. There may have been arsenic based systems and phosphorus bases systems, and they may have combined at different times and places, and most life subsequently evolved from a subset of these different bowls of primordial soup. One of those primordial soup bowls happend to be just like all the others but for the bit about arsenic. The test of this hypothesis (a partial test, anyway) would be to reconstruct the phylogeny of this bacterium. Did it separate from the other bacterial lineages at a time near the origin of life, or much more recently? Wolfe-Simon and her team are at present not saying anything about the phylogeny of this bacterium, and when asked about it at the press conference indicated that they just don’t know yet.

The second idea is more likely, and relates closely to the thrust of the research team’s presentation in their paper and in the press. At a large scale, arsenic substitution for phosphorus simply means that we should not be ignoring phosphorus-poor arsenic-rich environments on other planets. At en even larger scale, we should consider that other substitutions are possible (silicon for carbon is a common idea along those lines, at least in science fiction!).

But with respect to life’s origins on earth, related to Darwin’s second theory, there is a more direct implication that I think would be easy to explore. Irregardless of the phylogenetic position of this particular bacterium, its existence today suggests the possibility of the existence of something like it in the past. So, the question is, biochemically, is there either a stage in the origin of life in which arsenic is the key element for certain chemical activities in stead of phosphorus, or, more interestingly, can we find populations in one part of the ancient earth (as fossils, of course) of phosphorus based bacteria and other populations, in different geological regions, of arsenic-based bacteria, living contemporaneously?

Get cracking, ancient biochemists!

Wolfe-Simon, Felisa, & Et.Al. (2010). A bacterium that can grow by using arsenic instead of phosphorus Science : 10.1126/science.1197258

Comments

  1. #1 SocraticGadfly
    December 2, 2010

    This is breathless, if not outrightly bad, science, IMO. Arsenic had already been know to be part of “sugars” in some bacteria, for example. And, the researchers can’t even prove the arsenic replaced phosphorus?

    Excuse me if I don’t wonder if this isn’t part of a NASA push for Mars satellite money from a budget threatened with truncation. http://socraticgadfly.blogspot.com/2010/12/bad-or-at-least-breathless-science-by.html

  2. #2 Greg Laden
    December 2, 2010

    And, the researchers can’t even prove the arsenic replaced phosphorus?

    I’m sorry if I gave that impression. They have dead-on proof that the arsenic is in place of phosphorus in the DNA backbone. They have not investigated arsenic in every other place it could replace phosphorus, but the original experiment seems to require that arsenic is generally replacing phosphorus, but the definitive proof for each contest is not provided in this paper. There is a paper to be submitted in Feb that will cover that, I think.

    Yes, you raise a good question in your post about the long-scale time on substitution. But the sense of “cultivation” needs to be clarified. Are there any studies that show that bacteria not from arsenic lakes can be “cultivated” to substitute arsenic?

  3. #3 Jason
    December 2, 2010

    As a biochemist put me in the ‘intrigued, but not remotely convinced by most of these claims’ category.

  4. #4 greame
    December 2, 2010

    @SocraticGadfly
    What I find bad reporting is using Wikipedia as a source for your argument. While an intersting post, was wikipedia really the best you could do?

  5. #5 Stephanie Z
    December 2, 2010

    Frankly, I’m more upset that SocraticGadfly decided to huff and question motives based on how the discovery was written up in Gizmodo. I mean…Gizmodo!

    Okay, to break that down, Gizmodo is part of Gawker, an unabashed page-view generator. Their stuff is supposed to be breathless, or weird, or appalling, for just that reason. Beyond that, Gizmodo is a gadget (i.e., gizmo) site. It doesn’t bill itself as a science site, and I have yet to see a writer there bill themselves as a science writer or science blogger.

  6. #6 Patrick Hadley
    December 2, 2010

    Can I just thank you for such a well written and informative explanation? If only all science writers were as good as you.

  7. #7 Mingr
    December 2, 2010

    The whole thing seems to hold together – though I’d really buy into the ‘new life form’ if codons, or fundamental genetics were different.
    What I don’t get is, if you look at DNA (or whatever As based DNA is called) then it would have a slightly different structure with As instead of P, no? The charge distribution, etc., would have to be different, because As isn’t P. Now, consider DNA polymerase or any other enzyme. With slight changes to the charge distribution of DNA (As) the enzyme would also have to change somewhat to work properly. Even the substitution of As for P in the enzyme would (should ?) cause changes to the folding. It doesn’t have to be a lot, then the lock no longer fits the key.

    Look, I’m probably screwing this up – my last biochemistry lecture was in ’81 – but as I watched the Q&A, thats the problem I had: not so much the substitution, but the question as to the finely tuned enzymatic innards of a cell could still function.

    What am I missing?

  8. #8 Mingr
    December 2, 2010

    I hope this doesn’t double post, but I watched the stream live, and one thing that stuck in my mind was not substiting As for P, but that the charge distribution on enzymes and, say Arsenic DNA, would alter slightly. So, As is similar to P, but not exactly the same. So, DNA would have a slightly different shape and charge distribution, as would, say, DNA polymerase. So, DNA polymerase (and the countless other enzymes) would have slightly different active sites. Maybe most of these would work well enough, but in many cases, you expect the key would no longer fit the lock.
    Its been a long time since I sat through a biochem lecture, but what am I missing?

  9. #9 Greg Laden
    December 2, 2010

    What I don’t get is, if you look at DNA (or whatever As based DNA is called) then it would have a slightly different structure with As instead of P, no?

    A isn’t P but it is a neighbor on the Periodic Table. But it is different. Yet similar.

    Your question is basic to the next level of research on this thing. They need to turn on the physics, try to get an ESR model of the molecules with arsenic, if possible, or something like that

  10. #10 MadScientist
    December 2, 2010

    I’m not entirely convinced of the necessity for descent from a single organism (though that is certainly not impossible). The trouble starts as we wind back the clock – we go from multicellular to single-celled organisms. What could the common ancestor of a single-celled organism be like? Now we go back even further and lose the cell membrane. What kind of chemistry was going on then? At the very beginning some chemicals must have fortuitously combined to create self-replicating assemblies which could be modified with each replication. At what point does a self-replicating assembly get called an “organism”? Could a number of early “organisms” met up and combined to form a single organism or multiple similar organisms which was/were the ancestor/s to all existing life forms? What is certain is that there was at least one ancestor and that it was an ancestor common to all currently known extant life forms whether plant or animal. (But who knows – perhaps one of the early replicators used arsenic rather than phosphorous).

  11. #11 Greg Laden
    December 2, 2010

    Mad,you are essentially advocating my first hypothesis, which is good.

    The other thing I did not mention because this post was getting long is the gambler’s dilemma.

    For all we know there were thousands of origins, each at some point developing to a form that could not integrate with other, parallel forms with different origins. Multiple threads of life at once.

    Following this, every one of them would have a high chance of going extinct, just like each of the gamblers sitting at a poker table, continuously playing and betting, not able to obtain money other than the finite amount they came to the table with. Every now and then one of the gamblers would hit the ‘vanishing line’ (zero dollars) and leave the table. Eventually there would be one.

    To me, it seems very likely that if life can exist at all (and it can, apparently) it can start up multiple times in perhaps multiple ways, but all the different lineages would go extinct leaving only one left

    The reason there are not new origins (new poker players showing up at the table over time) is that early life also created conditions not conducive to new life forming.

    Or maybe it does now and then ….. (But there is no evidence of that at this point)

  12. #12 David Horton
    December 2, 2010

    I may well be misunderstanding something, and you do touch on it with questions about phylogeny. But why isn’t this simply a late adaptation to a very unusual, arsenic rich, environment? We know bacteria can evolve to meet all sorts of extreme environments – deep ocean “smokers”, low oxygen muds, deep rocks, high sulphur areas, high or low temperatures – why is this so exciting?

    And in relation to exobiology, well, we know that it is theoretically possible to substitute all kinds of elements for others close on the periodic table, and to have some of these alternatives being favoured by natural selection on a planet with a somewhat different chemical make-up to ours seems, well, a no-brainer.

  13. #13 David Marjanović
    December 2, 2010

    http://dx.doi.org/10.1126/science.1197258 does not exist (yet?).

    So, all I can say… if it has substituted As for P in part of its DNA, that means it has DNA in the first place. And that is pretty strong evidence for common ancestry. There are so many other bases and so many other backbones that are possible, and many have been created in the lab and shown to work in principle, yet only RNA and DNA occur in Life As We Know It.

    That the substitution is partial clinches it as far as I can tell without access to even just the abstract.

    Regarding locks and keys, locks don’t need to fit their keys perfectly. Evidently, in this bacterium, they don’t. Furthermore, lock-and-key is a less precise model than induced fit: enzymes swim around in a partially unfolded conformation, and when the substrate comes along, they wrap around it and assume the “lock” shape. The active center (which does the actual catalysis) only exists when the enzyme is in the “lock” conformation.

  14. #14 David Marjanović
    December 2, 2010

    In short, I agree with comment 12.

    And I forgot to mention that http://scienceblogs.com/gregladen/2010/12/10.1126/science.1197258 of course doesn’t exist either – that’s where the link in the reference leads!

  15. #15 Greg Laden
    December 2, 2010

    http://dx.doi.org/10.1126/science.1197258 does not exist (yet?). Keep trying.

    David: I may well be misunderstanding something, and you do touch on it with questions about phylogeny. But why isn’t this simply a late adaptation to a very unusual, arsenic rich, environment?

    That’s what it is, pretty much for sure.

    if it has substituted As for P in part of its DNA, that means it has DNA in the first place. And that is pretty strong evidence for common ancestry.

    Absolutely. That is what I conclude as well. But this is not a finding without implications. Sorry for the double negative.

    Regarding locks and keys, locks don’t need to fit their keys perfectly.

    That is true. But for a while at the cabin we had a lock that would open with any one of a dozen different keys. That potentially changed things, it certainly changed the way we locked that door (we needed to use the deadbolt instead of the knob lock). Also, my garage door opener opens my neighbor’s garage door one in five times. Imagine the possibilities there!

  16. #16 Greg Laden
    December 2, 2010

    Huh;.. that’s an automatically generated link. I can’t seem to fix that for now, but here’s the Science link:

    http://www.sciencemag.org/content/early/2010/12/01/science.1197258

  17. #17 David Horton
    December 2, 2010

    “a late adaptation to a very unusual, arsenic rich, environment?
    That’s what it is, pretty much for sure”

    Yes, I thought I must be missing something, that NASA had somehow eliminated the possibility of a late adaptation. It seems to me irresponsible to make announcements in this form – media outlets here were picking up on the “aliens are among us” apparent suggestion. Now I know media outlets and their reporters are incredibly dumb when it comes to science matters, but the NASA announcement seemed to me to deliberately court this kind of misunderstanding, deliberately setting it up to be sensationalised. And I thought a bit better of NASA than that.

  18. #18 Greg Laden
    December 2, 2010

    Their press release said almost nothing. Just that there was an important announcement in astrobiology, with a list of participants. I think this kind of thing happens no matter what you do, and in this case, they may have tried to say as little as possible.

    Also, I do not accept the idea that using a new and interesting finding for the sake of positive publicity is somehow wrong. I often see the most vehement negative comments about that sort of thing come from the same people who want the free market to organize everything for them. But if a manufacturer comes out with a new product, they don’t release it right away .The release it with consideration of timing and in a manner that maximizes interest in the product. Why is it OK for private free marketeers (and others) to maximize interest in what they are dong but scientists not?

    Pretty much the same complaints are being made about this press event as were made about Ida, and the two define opposite and extreme ends of a spectrum. Ida: An entire book released at the same time as the press conference, huge publicity preceding the press conference, all that missing link talk, etc. etc. With this one, a three line press release and that’s it.

    If both of those approaches are elicitin the same complaints, I’m staring to wonder about the complaints themselves.

  19. #19 SocraticGadfly
    December 2, 2010

    @Greame – First, Pharyngula has similar info on arsenic already being known in biological processes and chemicals.

    Second, the first two or three references on that Wiki page are all National Academy of Sciences. Got something against it, too? The three footnotes on the arsenic section prior to this story come from the University of Minnesota, NIH, and New Scientist. Got problems with all of them, too?

    Third, I don’t get why people have a blanket condemnation of Wikipedia. On current events/politics/living history, YES. But, in general, in the natural sciences, in more ancient history, and many other areas, Wikipedia is pretty reliable.

    @Stephanie Z … it wasn’t JUST Gizmodo. I also linked the New York Times’ story and others. I did forget to include the “breathless” part there, which Overbye had in his first graf:

    “Scientists said Thursday that they had trained a bacterium to eat and grow on a diet of arsenic, in place of phosphorus — one of six elements considered essential for life — opening up the possibility that organisms could exist elsewhere in the universe or even here on Earth using biochemical powers we have not yet dared to dream about.”

    Since I posted that story, I also see that Phil Plait at Discover has given into the “breathlessness” a bit much.

    Finally, where’s your skepticism at WHY this story was overhyped by NASA in the first place?

  20. #20 David Horton
    December 2, 2010

    You are obviously a kinder man than me Greg. Maybe I am misjudging NASA from what you say, but it seems to me that scientists, in a science-ignorant media world, need to be very careful to avoid sensationalising findings. You are right, the Ida thing was especially bad, but I hate hearing “are aliens among us?” headlines when the actual finding was a lot more low key, in fact so low key as to be almost not worth making. Life may be possible on a range of fairly un-Earth like planets? Well, D’oh.

  21. #21 Donna
    December 2, 2010

    Arsenic substituting for Phosphorus and not killing the organism? That’s a major headline no matter how you cut it. NASA did not mislead the press on this. As stated, their pre-press release said almost nothing and all that hype was generated by the media.

  22. #22 David Marjanović
    December 2, 2010

    But this is not a finding without implications.

    Oh, indeed not, see comment 21.

    As stated, their pre-press release said almost nothing and all that hype was generated by the media.

    Because the pre-press-release was worded carelessly enough to allow such hype. “Something to do with the possibility of extraterrestrial life” didn’t make me expect that extraterrestrial life had been discovered, but it did make me expect more than an otherwise completely unremarkable basophilic Bacterium As We Know It that can substitute As for P.

    That’s what I take issue with. It’s completely fine to generate suspense, but it shouldn’t outright mislead. In business, misleading too strongly is punishable.

  23. #23 Tim Gorski
    December 2, 2010

    If the codon-language is the same then the substitution for arsenic would be almost certain to have happened later. I.e., the arsenic-for-phosphorus organism(s) would be descended from the same ancestor that “normal” organisms are.

  24. #24 Greg Laden
    December 2, 2010

    I think it is sad, and avoidable, that the science blogosphere will focus on the nature of the press release and the nature of the inappropriate response by the press rather than the science. This is becoming a pattern.

    Folks, the press is ALWAYS going to fuck it up. It doest not matter what the scientists or science agencies do. If the main thing the science blogosphere can communicate to its collective readership is that press releases are bad and the non-science or marginally science press (e.g. Gawker) is bad whenever a major science finding is announced, then the readers of said blogosphere might as well stick with standard science news outlets like the science section of the New York Times.

    I intentionally wrote a post that looked at certain aspects of this research that I knew no one else would focus on, and mostly avoided discussion of the press aspect of the work (there are one or two not too well hidden references to that but that’s it).

    Nothing wrong with criticizing the press, or the press-releases or press offices. But if that is the only or the main reaction a group of science communicators has to virtually every finding that comes along (and my exaggeration level here is only about 50% or so) than why bother with it?

    It’s like calling a Nascar race and talking only about how loud it is and not noticing when the first five cars race across the finish line. In fact, this situation is so bad, I’m using Nascar analogies! Help me!!!!

  25. #25 Jim Thomerson
    December 2, 2010

    I know nothing about bacterial phylogeny or classification. However, a classification is an hypothesis of evolutionary relationship. The bacterium in question is “strain GFAJ-1 of the Halomonadaceae”, which implies that it has a number of related strains within that family. It is not a big outlier, just a bit unusual. Now it may turn out that this classification does not accurately reflect its evolutionary relationships. That will be interesting to follow.

  26. #26 idlemind
    December 2, 2010

    Like Jim I’m ill-informed on matters of bacterial classification, but it would seem that the fact that the bacterium is identified as a member of a known family of bacteria unambiguously rules out any claim of it being some wholly new form of life. But like the discovery of thermophile bacteria in deep ocean vents, it broadens our knowledge of the range of conditions under which life can exist. It’s not the silicon-based life of science fiction, but it does tend to support the claims of exobiologists who say that conditions for life aren’t as fine-tuned as some skeptics claim.

    NASA sees this as bolstering the search for extraterrestrial life by enlarging the set of chemical processes that support it. I don’t see any reason to deny them that claim. Arsenic-tolerant bacteria is one thing, but substituting As for P in DNA seems like a pretty big deal.

  27. #27 Stephanie Z
    December 2, 2010

    SocraticGadfly, if you’d like to complain about NASA’s hype, complain about something NASA did, please.

  28. #28 Greg Laden
    December 2, 2010

    Jim, that is how it is classified, but a focused phylogenetic study has not been done or reported, so we need to avoid making assumptions . It may be that there is a whole category of bacteria that do this arsenic thingie and they are all related to each other, or this one type could be fairly unique. Bacteria are rather promiscuous in their gene exchange, and they even ‘absorb’ into their lineages genes that are not even bacterial genes (soil bacteria often have animal genes, modified, for instance …. having found them lying around in the soil presumably). So phylogeny with bacteria may not be a very pretty picture.

  29. #29 Greg Laden
    December 2, 2010

    it broadens our knowledge of the range of conditions under which life can exist.

    Yes, that is certainly the main conclusion.

  30. #30 SocraticGadfly
    December 3, 2010

    Greg, I don’t think it’s so much, and certainly not solely, the science press screwing this up.

    I think that, in addition to some fluffing, there was probably some rushing by NASA.

    The best – and most skeptical – coverage is from Nature. It’s definitely worth a read:

    “It remains to be established that this bacterium uses arsenate as a replacement for phosphate in its DNA or in any other biomolecule found in ‘standard’ terran biology,” says Steven Benner, who studies origin-of-life chemistry at the Foundation for Applied Molecular Evolution in Gainesville, Florida.

    Arsenate forms much weaker bonds in water than phosphate, that break apart on the order of minutes, he says, and though there might be other molecules stabilizing these bonds, the researchers would need to explain this discrepancy for the hypothesis to stand. Still, the discovery is “just phenomenal” if it holds up after further chemical analysis, Benner adds. “It means that many, many things are wrong in terms of how we view molecules in the biological system.”

    And …

    To be truly convincing, however, the researchers must show the presence of arsenic not just in the microbial cells, but in specific biomolecules within them, says Barry Rosen, a biochemist at Florida International University, Miami. “It would be good if they could demonstrate that the arsenic in the DNA is actually in the backbone,” he said.

    Also, he says, the picture is still missing an understanding of what exactly the arsenic–phosphorus switch means for a cell, says Rosen. “What we really need to know is which molecules in the cell have arsenic in them, and whether these molecules are active and functional,” he says.

    For example, if phosphate in ATP was exchanged for arsenate, would the energy-transfer reaction that powers a cell be as efficient? In metabolic processes in which arsenate would bind with glucose, would the bonds it forms — weaker than those of phosphate — be as effective? And phosphate groups bind to proteins modify their function, but would arsenate work as well?

    http://www.nature.com/news/2010/101202/full/news.2010.645.html

    That all said, theoretically, yes, this could point to multiple evolutionary pathways. But, given that the bacteria force-fed arsenic grew only 60 percent as fast as their natural cousins, in a controlled and protected lab environment, I highly doubt that, unless many other variables also changed, an arsenic-instead-of-phosphorus evolutionary line actually would be successful.

  31. #31 CFD Trading Strategies
    December 3, 2010

    The “One Long Argument” by Ernst Mayr is for sure a hit. I don’t think Darwin has its second theory. But whatever it is. I’m sure this book contains more fun. I’m also interested with how he breaks down the body of thought into five separate and distinct theories. I’m looking forward to it.

  32. #32 intercostal
    December 3, 2010

    So phylogeny with bacteria may not be a very pretty picture.

    >

    THAT’s an understatement.

    I wonder if it would not be more practical to use purely phenetic classifications for groups with too much horizontal gene transfer? The concept of a single phylogenetic tree becomes problematic.

  33. #33 IanW
    December 3, 2010

    It’s always nice to see some science on science blogs. Good job!

  34. #34 Greg Laden
    December 3, 2010

    They ARE claiming that the arsenic is very likely in the backbone of the DNA. The February paper may solidify this. One often finds the most severe critiques of a Science paper dug up by the Nature editors, and visa versa. Which is a good thing. There would actualy be a problem if one or the other journals went under, though both should be Open Access!!!

  35. #35 Tulse
    December 3, 2010

    A tangential point, and not to pick nits with someone like Mayr, but Darwin did famously write:

    “There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one”

    Darwin here is explicitly acknowledging the possibility of multiple abiogenesis events. As long as those events were relatively uncommon, and that the resulting organisms then followed descent with modification, I don’t see how Darwinian evolution requires a single origin. Even if our arsenic-friendly beastie turned out to be completely unrelated to all other currently-known organisms on the planet, we would surely be right in presuming that it evolved from earlier less-complex organisms, back to a very simple organism that arose from non-biological processes.

    The number of abiogenesis events on this planet (or any other) is merely a contingent fact, not a necessary principle of the theory of natural selection. (What is a necessary principle is that such events could only produce organisms of the most simple kind, organized purely through chemistry and physics — abiogenesis won’t produce a tiger.)

  36. #36 sex hikayeleri
    December 3, 2010

    The “One Long Argument” by Ernst Mayr is for sure a hit. I don’t think Darwin has its second theory. But whatever it is. I’m sure this book contains more fun. I’m also interested with how he breaks down the body of thought into five separate and distinct theories. I’m looking forward to it.

  37. #37 Greg Laden
    December 3, 2010

    Tulse, yes, he does say that. There are others of his “five theories” for which one can find contradictory statements, in large part because Darwin did in fact change his mind a number of times about a number of things.

    But also because “common descent” is a weak assertion and not an important one. It is important that all animals and plants and stuff are from a common ancestor, but the idea of more than one line of life staring off …. metaphorically breathed at by god, as it were … isn’t really explicitly ruled out by Darwin, and is suggested here, but he does talk about common descent of all known forms and discusses evidence for that.

    At the time, though, he did not have the best evidence at hand, which is molecular.

  38. #38 D
    December 3, 2010

    They are claiming that arsenic is being integrated into the DNA backbone, but they didn’t really prove it yet.

    A lot of their data is pretty indirect, and doesn’t really go very far towards showing that arsenic is actually being used for anything useful.

    Show me the mass spec. with nucleotides, proteins, etc. that have arsenic in them, and I’ll be a lot closer to buying this. (The only mass spec they had was on fractions from purification steps, which is hardly compelling data.)

    As for phylogeny, this bug is pretty darn close to a lot of familiar bacteria…

  39. #39 Alan Kellogg
    December 3, 2010

    Similar is not the same, arsenic is not the same as phosphorus, if it were life would substitute it for phosphorus on a ready basis. Frankly, I wouldn’t call what GFAJ-1 has DNA. It may perform the same functions as DNA, but using arsenic where DNA uses phosphorus makes it something else entirely.

    As far as I can see this is a subject that calls for further research. If I am right it means we have discovered a new domain of life, one that uses arsenic where we belong to a phosphorus using domain. But, again, further work is called for.

  40. #40 Ormond Otvos
    December 3, 2010

    “it does tend to support the claims of exobiologists who say that conditions for life aren’t as fine-tuned as some skeptics claim.”

    In the real world, this is the important observation.

    Competing Gods, anyone?

  41. #41 CLS
    December 3, 2010

    [i]“That all said, theoretically, yes, this could point to multiple evolutionary pathways. But, given that the bacteria force-fed arsenic grew only 60 percent as fast as their natural cousins, in a controlled and protected lab environment, I highly doubt that, unless many other variables also changed, an arsenic-instead-of-phosphorus evolutionary line actually would be successful.”[/i]

    You don’t need too many other variables, they already come from a selective environment rich in As. It would be interesting to know what else lives in the lake. However, there are an abundance of reasons for it to survive among relatives at lower growth rates (not to mention that the lower growth rates are at experimental concentrations of arsenate 200x higher than the average in the native environment).

  42. #42 Greg Laden
    December 3, 2010

    The growth rate is not a measure for whether or not there is an adaptation, or for how interesting something is! It may well be that in A+/P- habitats, you get slow growth rate. So what?

  43. #43 Jim Thomerson
    December 3, 2010

    The Mono Lake brine shrimp are an endemic species. You can purchase Mono Lake brine shrimp eggs to hatch out to feed you baby tropical fish, as well as frozen adult Mono Lake shrimp, said to be more nutritious than San Francisco Bay or Great Salt Lake brine shrimp.

  44. #44 Devin Trudeau
    December 3, 2010

    This discovery doesn’t have any relevance to common descent. Obviously the bacteria is related to all known life on earth.
    It also hasn’t been proven that arsenate is in the DNA backbone, rather than associated with the DNA in some other way.
    The most important thing that this study showed, IMO, is that arsenate could be used to replace some of phosphate’s roles (but we still don’t know which).

  45. #45 Richard S.
    December 3, 2010

    This discovery doesn’t have any relevance to common descent.

    The discovery or the organism? The organism, certainly not.The discovery, well, the argument has been made but I’m not sure you read it. Damn Laden and his posts too long to get through.

  46. #46 Tulse
    December 3, 2010

    It is important that all animals and plants and stuff are from a common ancestor

    Perhaps I’m misunderstanding your point, but I’m not clear as to why it is important in principle for the theory of evolution. Surely if this critter proved to be descended from a second abiogenesis event (which it most clearly isn’t), that wouldn’t suddenly invalidate natural selection. We have very good evidence of common descent of all known organisms, but if we found some tucked-away niche somewhere with a “shadow biome” of organisms not related to those we know, it would be interesting, but no more problematic for evolution than if we found such organisms on Mars or Europa or Titan (or Enceladus, or Gliese 581g, or…). We’re happy in those cases to consider that such organisms share no common descent with those we currently know, without that violating Darwinian principles, so why not in a potentially isolated niche on this planet?

  47. #47 SocraticGadfly
    December 4, 2010

    Greg, more argument against your support for this angle:

    From a commenter at Pharyngula:

    1) The best As:P ratio they got was 7.3:1 in dry cell weight. They are using media with phosphate contaminants (~3 uM). The extremely slow growth rate (20-fold in six days; compared to E. coli roughly 20-fold in 90 min) suggests limited growth that is occurring from phosphate salvage. …

    3) There is no evidence that As is incorporated into functional DNA or RNA and that such As-nucleotide is competent in replication/translation. They have evidence that As is incorporated into nucleic acids. That’s a major leap from there to functionally competent DNA/RNA.

    4) Arsenate diesters are unstable in water. The hydrolysis rates for arsenate esters are 10,000 – 1,000,000 times faster than the corresponding phosphate esters. No stability; no genetic information. The notion that water is kept away is curious at best and the hallmark of pathological science at worst. …

    6) It’s been known that arseno-ADP, the ATP analog, is not stable in water. … How do you get to arseno-DNA without arsenic analogs of ATP?

    So, sorry, Greg, nice try but I think you’re flogging a dead horse. NASA definitely is.

  48. #48 Greg Laden
    December 4, 2010

    tulse: Please look at the phrase before the one you quote: “”common descent” is a weak assertion and not an important one.” and also the rest of the comment and also the post I wrote.

    We are in agreement: Multiple origins does not obviate or in any way challenge basic evolutionary theory.

    However, Darwin recognized, as do we all, that the actual history of life itself is interesting and important, and he reasoned and apparently correctly that all the forms he was familar with on Earth came from a common ancestor and indeed this observation is important for another reason: It freaks people out who don’t want to even think about “apes (or fish or whatever) evolving into clergymen (or whatever)” (so there is pragmatic political importance to the ancestral relationship between, say, mushrooms and your Aunt Tillie, and Darwin was acutely aware of that)

    But again (and again and again) the other four of Darwin’s theories, and/or any other way you want to conceptualize Darwinian theory (most people think mainly of Natural Selection), if there were multiple origins (and there may have been, and as I suggest in my post, this new research finding suggests a methodology for testing for that, perhaps) it does not matter.

  49. #49 Greg Laden
    December 4, 2010

    SG: “Greg, more argument against your support for this angle:”

    What angle? How could you possibly be under the impression that I have “an angle” … I’ve discussed no fewer than a half dozen different ideas in this post. You’re going to have to be more specific. But I can deal with some of your questions.


    1) The best As:P ratio they got was 7.3:1 in dry cell weight. They are using media with phosphate contaminants (~3 uM).

    Yes, I read the paper. In my view it remains to be seen as to weather this is important or not. The authors make the claim that this is unprecidented and indicates the possibility of A substituting for P (remember, that is what they are looking for) There are thus two ways to evaluate this. 1) Is it really the case, as the researchers say, that this is impressive, or is it the case as Larry Moran claims that we already knew that organisms did this. Quite possibly the researchers are being overoptimistic and Larry is being a curmudgeon. And 2) Even if this is run of the mill bacterial activity (which I doubt) is it the case that we’ve underestimated the viability of life in A+/P- habitats?


    The extremely slow growth rate (20-fold in six days; compared to E. coli roughly 20-fold in 90 min) suggests limited growth that is occurring from phosphate salvage. …

    I really don’t understand why people keep mentioning the rate of growth. So what? Growth rates are adaptive features. Why is a high growth rate somehow associated, teleology-like, with better results or some argument that something is more adaptive or more real? Do you understand what growth rates are? The growth rate thing is a red herring.

    3) There is no evidence that As is incorporated into functional DNA or RNA and that such As-nucleotide is competent in replication/translation. They have evidence that As is incorporated into nucleic acids. That’s a major leap from there to functionally competent DNA/RNA.

    They make the specific claim that A is incorporated in the DNA in replacement of the P backbone. They say they suspect that A is incorporated into a wider range of locations, and they say they have more evidence in an upcoming paper.

    4) Arsenate diesters are unstable in water. The hydrolysis rates for arsenate esters are 10,000 – 1,000,000 times faster than the corresponding phosphate esters. No stability; no genetic information. The notion that water is kept away is curious at best and the hallmark of pathological science at worst. …

    I don’t know what to say about your accusation of pathology, but you have exposed a contradiction here. If they have evidence that A is doing something all the smart people know it CAN’T do, then why are all the smart people saying that nothing they’ve claimed A to be doing is something that we didn’t already know that A did? The whole point of this research is that something unexpected is happening, and that A might be managing to do things we thought only P could do . Your incredulity is fine, but irrelevant to the fact that claims running uphill against widespread incredulity are being made. What this means is that we need to see further investigation and replication.


    6) It’s been known that arseno-ADP, the ATP analog, is not stable in water. … How do you get to arseno-DNA without arsenic analogs of ATP?

    Again, your argument from incredulity does nothing more than to sharpen the potential significance of a finding that seem impossible.

    So, sorry, Greg, nice try but I think you’re flogging a dead horse. NASA definitely is.

    Well, let’s be clear about three thigns.

    1) You did not read my post. You’ve listed a bunch of things that you don’t like about the paper, not related to what I wrote about above.

    2) They said “Everyone knows A is dogma and B is impossible. We found evidence that B is not as impossible as we thougth” and your response, quite literally, is to say “B can’t be less impossible than we thought, because we already thought it impossible!”

    3) You have not explained your motivation for insisting that there is nothing to see here. Would you care to?

  50. #50 Anonymous
    December 4, 2010

    A very interesting article but Darwin’s theories are child’s play compared to the actual origin of replicating life. It’s the ultimate chicken and egg argument and to date no one has a remotely plausible explanation. In the biology books this is ignored and glossed over as if it’s a minor technical detail. But in fact evolution is the “minor detail” compared to the creation of life from simple inorganic matter. I profess no answers but suggest more humility about how little we understand this process.

  51. #51 Henry Harris
    December 4, 2010

    A very interesting discussion, but aren’t we missing the big picture here? What this discovery implies is that chemistry doesn’t matter so much as the physics, and, as far as we know, physics is a constant throughout the entire universe. The implications of that simple fact boggles the mind. It implies there is an intimate connection with life and the existence of the universe itself. Life can’t be an accident if its an emergent property of fundamental physics.Obviously there’s something very fundamental we don’t understand.

  52. #52 Greg Laden
    December 4, 2010

    Anon: I agree completely. Or, at least, the question is humbling and the answers are distant. It may be that once we have a handle on it, it will be one of those “Oh THAT is how it works! Of course, how simple and straight forward!” moments.

    But there is an explanation for why origins are so unclear. It is an ancient event the relevant evidence for which is hard to find and interpret because of billions of years of erosion, diagenesis, and dramatic changes in environmental context … life originated, however it did that on an Earth much unlike the one we live on now. Meanwhile, the total amount of research dollars spent on this particular topic could barely pay for a single battery of Patriot Missles or a single week of cancer research globally. Or something (I have no idea what the numbers really are but certainly along those lines)

    If we spent the same effort on origins as we do on any of the best 100 funded research topics, we’d have it nailed down now. We’d be making life in the lab. We’d probably have exhibits in science museums where visiting school children can make life.

    But we won’t let them take it home.

  53. #53 Stuart Young
    December 4, 2010

    I agree to some extent but major scientists all over the world have looked at this for 50 years utilizing modern scientific labs. I don’t think this is primarily an issue of funding since there are no workable theories to pursue currently. I find it interesting that the Nobel level experts openly admit that science currently has no plausible explantions and in honestmoments of reflection the great men admit to being completely baffled. Hence panspermia and crystals and all the other “mystical” answers. As I said before this is not some minor issue that can be explained away. Evolution is but a tiny grain of sand once replicating DNA exists compared to creating sustainable life from inorganic material. It is a great deficiency of the modern scientific education establishment that so few “educated” students are remotely aware of this dilemma and instead believe that it is largely understood.

  54. #54 Greg Laden
    December 4, 2010

    I agree to some extent but major scientists all over the world have looked at this for 50 years utilizing modern scientific labs.

    No, they haven’t. Has there been a single funded center to do this work? An RTG program? An interdisciplinary research center at a major research university? The total amount of work in this area is very very little.

    I don’t think this is primarily an issue of funding since there are no workable theories to pursue currently.

    Huh?

    There are lots of theories, hypothees, and ideas. I myself proposed one once that is out there in the literature somewhere. Very broadly, there are the contextual theories (thermal/vents, primordial soup, cooler vs hotter earth, etc.) cell-related theories (cells first, replicators first), differing ideas about the nature of replicators, was it protein like molecules messing around that got r/dna, or was it rna/dna like molecules first that got proteins (I prefer the latter), and so on and so forth.

    Every one of these ideas (hypotheses/theories) is associated with some kind of field work, lab work, modeling, etc.

    I find it interesting that the Nobel level experts openly admit that science currently has no plausible explantions and in honestmoments of reflection the great men admit to being completely baffled.

    That is a fairl specific statement that requires references, non-quote mined quotes, and some good context indicating that the individuals referred to have not been cherry picked. Good luck with that.

    Hence panspermia and crystals and all the other “mystical” answers.

    Panspermia is actually a great example to bring up in this context. A totally dumb theory proposed by someone with a big name but not a lot of data or good research to back up the data, which was NOT more or less immediately shoved aside.

    Compare the paper discussed in this post with panspermia. Dozens have openly raised valid (to varying degrees) questions about the paper, because there are zillions of scientists, research labs, papers, etc. focusing just on the biochemistry of organic molecules and cellular systems. In contrast, some dumb idea about the origin of life gets to live a hapless zombie like existence because there are hardly any zombie slayers.

    Thus, the conundrum of many “thories” and few answers.

    Evolution is but a tiny grain of sand once replicating DNA exists compared to creating sustainable life from inorganic material.

    How do you know? Since you don’t know how live got started, how do you know it wasn’t a very simple series of events on a primordial earth? Remember, again, that the earth on which life started may as well have been a different planet. Since we don’t know how it started, we don’t know if it is some amazing event or a run of the mill series of reactions.

    It is a great deficiency of the modern scientific education establishment that so few “educated” students are remotely aware of this dilemma and instead believe that it is largely understood.

    Actually, I think it might be just you. Have you read any text books lately? The current theories (of which you are clearly unaware) are discussed, problems and possibilities are discussed, the fact that we don’t really know but have some interesting ideas is discussed.

    I’m talking about textbooks and stuff, not web sites you may have run into. If you google “origings of life” you get mostly crap. Might as well google “bigfoot”.

  55. #55 Anonymous
    December 4, 2010

    Are you really suggesting that the biochemists the world over have just ignored this issue for the past 50 years? As for funding the combined labs of the world have spent large amounts of money over the years and could have easily pusued this if there were good researchable ideas. After all a certain Nobel awaits and this would be the greatest scientific discovery of all time. To claim it hasn’t been discovered for lack of research funding is not credible. Besides why then haven’t the private labs pursued this? Controlling the creation of new life would be yield untold fortunes to the inventor. As for the new theories please tell me what they are? Thermal heat vents, primordial soups, etc are not real scientific theories but more like fairytales. A real theory has to explain how relatively randomly dispersed inorganic molecules could come together in a very specific structure to create replicating life without any proteins. I have read all the theories about RNA etc. But again this does not remotely answer the question because no can explain where the single stranded self replicating RNA came from. If you have a pausible theory I have missed I very much would like to learn about it. I have an advanced degree in a scientific field and I have never read a single paper that could offer even a hint of a process that could reproduce life from inorganic material.

  56. #56 Greg Laden
    December 4, 2010

    Are you really suggesting that the biochemists the world over have just ignored this issue for the past 50 years?

    Is that my only choice? Ignored? I’m not sure what that means. Evolutionary theorists, various sorts of biologists (not just biochemists) have had access to very little funding to carry out this research. Most major research questions are addressed by the funding of numerous major research and graduate training centers, abundant grant money distributed in a merit-bases system via a number of different channels, has an industry and and an academic component, etc. This has not happened for origins of life research because it is not disease, a health related thing, seen as directly related to some industrial application, etc. Honestly.

    As for funding the combined labs of the world have spent large amounts of money over the years and could have easily pusued this if there were good researchable ideas.

    No, they haven’t.

    After all a certain Nobel awaits and this would be the greatest scientific discovery of all time.

    Are you imagining that there is a “discovery” that a person could make that is the origin of life? I doubt that very much. Could a person get a Nobel for making a significant advancement related to the origin of life? That’s possible. Maybe Manfred Eigen would get one. Or maybe Siney Altman or Thomas Cech.

    To claim it hasn’t been discovered for lack of research funding is not credible.

    Name the research centers. Tell me what percentage of, say NIH money or NSF money goes towards this. Name the top ten universities in the United States with the origin of life as one of their top three areas of study and training. No, my claim is not only credible but obvious.

    Besides why then haven’t the private labs pursued this? Controlling the creation of new life would be yield untold fortunes to the inventor.

    Some of the more interesting work in this area, recently, has been done in private labs, but they tend to be the ones funded by extravagantly rich individuals (who are not so rich any more) and they haven’t been able to fund at the level necessary. Almost all privately funded research, and there is a huge amount of it, is funded by investors who want to see how their money will be paid back. “controlling the creatoi of new life” and “untold fortunes” are great terms to use in getting the average schmo to invest a few bucks but real investment specialist go for pharms and other more certain targets.

    As for the new theories please tell me what they are? Thermal heat vents, primordial soups, etc are not real scientific theories but more like fairytales. A real theory has to explain how relatively randomly dispersed inorganic molecules could come together in a very specific structure to create replicating life without any proteins.

    So, you have shown your true colors as not only a sock puppet but also an Intelligent Design creationist.

    Why am I wasting my time? I have a new textbook to review for a major publisher. It has a chapter on the origin of life. That will be a fun read about now.

  57. #57 Stuart Young
    December 4, 2010

    Your response is mainly just a personal attack rather than a serious rebuttal of my points. How in the world did intelligent design get into the discussion? You said in your post that there were new plausible theories yet you never mentioned a single one. Moreover to claim there is no research money to discover the origin of life is patent nonsense. The world is filled with private companies that would immediately fund any project that could possibly create life from inorganic material since it would be of incalculable value. Once again please post a plausible theory about how this process began. Look not having an answer just points out how little we know and highlights what I said in my previous posts. There is no need to attack bacause I have made obvious points well known to everyone who has studied this subject. I am not promoting a god answer but to claim there is a sound scientific theory the scientist is required to make at least a plausible explanantion.

  58. #58 Greg Laden
    December 4, 2010

    Your response is mainly just a personal attack rather than a serious rebuttal of my points

    No, it is not. You have claimed that there are no ideas. I told you about the ideas. You have claimed there has been a lot of research done, I said no, you claimed again (and again) that there was, I noted that the absence of any evidence in the form of research centers, U’s that focus on this, etc. and challenged you to provide counter evidence. You have not .

    I’ve refuted each of your points up to the part where you spilled out the standard, old, tired, run of the mill, uninteresting, idiotic, canned, got-it-from-answers-in-genesis-web-site drek-filled argument, and that is when I told you that I was not interested in discussing THAT. Why should I?

    You have not experienced a personal attack from me. You’ll know it if it happens, I assure you.

    I am not promoting a god answer but to claim there is a sound scientific theory the scientist is required to make at least a plausible explanantion.

    If I had any faith at all that you had an inkling what the word “theory” meant, then I’d answer this question with this: Correct, there is no “sound scientific” theory of the origin of life, in my opinion. There are a number of good ideas, a number of hypotheses, that I’ve alluded to above. I am not a homework doer, an answer man, an on-demand bloggers, so don’t expect me to produce a bullet list for you beyond what I did. You could always look here … http://tinyurl.com/ffqpc .. like everybody else does, or here: http://tinyurl.com/2autj7z if you really want to learn something.

    But since I’m pretty sure you don’t know what the word “theory” means I’ll say this: Sure, there’s lots of “theories”, hypotheses, models, ideas, and so on. I gave you a brief mention of a few, you should have little problem doing the research to educate yourself on this topic.

    But no, actually, the problem is this. You believe that the primoridial universe was a random fully entropic chemical soup with absolutely no structure or unevenness and you require a theory of the origin of life to turn this int RNA.

    That is not what anyone thinks, but it is what ID creationists always start their origin of life argument off with.

    Then, when someone points out that they are merely ID creationists, they say “Oh, no, I’ve not mentioned anything about god, and you’re just personally attacking me and not dealing with the facts bla bla bla”

    Yeah, we’ve been there, done that.

    If you really are not an ID creationist, then you just now found out that you sound exactly like one and should be able to feel the chagrin. If you can’t feel the chagrin, you can’t learn.

  59. #59 Stuart Young
    December 4, 2010

    When I said evolution is but a small grain of sand compared to origin of life the polar/grizzy bear hybrid is a great example. We now know that these bears despite their significant differences are really just expressing the ranges of genes already contained in the bear chromosomes(no mutations required). So it’s not difficult to see how over another few hundred thousnd years or more a true new species could develop. This is not a difficult concept and gives strong evidence as to how evolution in bears works.

  60. #60 Greg Laden
    December 4, 2010

    really just expressing the ranges of genes already contained in the bear chromosomes(no mutations required).

    No they aren’t. They are distinct populatios. A polar bear never gives birth to a brown bear or visa versa. There were mutations, there was selection thereof, and lo and behold, polar bears are different from the other brown bears and are a good example of a recently evolved species.

    But yeah, as you say, it’s a great example of evolution and adaptation.

  61. #61 Henry Harris
    December 4, 2010

    At the risk of being obvious I would offer the following:

    Since we know, as I stated above, life can’t be an accident if it’s an emergent property of fundamental physics, it would seem to me that’s a place to start. Attempt to create a computer simulation that favors life knowing what we now know about physics. Unless there is some mystical “hand of God” involved there must be some artifact in the physical world that contains a clue of how life is favored. My confidence that this will work is based on the knowledge that it’s always worked before. If it were me, I’d start by looking at the recently discovered arsenic-based life and look for physical mechanisms that somehow relate/translate to those of ordinary life. My bet is there will be clues that will lead to a theory of undiscovered mechanisms that favor life over a range of chemistries. We can argue if they were put there by God later.

  62. #62 Jack Bauer
    December 4, 2010

    “Irregardless”? C’mon, that’s not a word!

  63. #63 Jack Bauer
    December 4, 2010

    “Irregardless”? C’mon, that’s not a word!

  64. #64 Tulse
    December 4, 2010

    The world is filled with private companies that would immediately fund any project that could possibly create life from inorganic material since it would be of incalculable value.

    How so? There is clear immediate value in genetic engineering and synthetic organisms, as Venter is pursuing, but any completely novel created life would be far less efficient at doing almost anything for quite a long time, until a lot of basic research had been done. Creating life by standard means (you know, critters reproducing) is likey to be far more productive for quite some time. Private companies for the most part don’t do basic research with such speculative payoff, especially when paths like Venter’s show far more immediate promise.

    Your comment is just silly, but I suspect you know that.

  65. #65 Stuart Young
    December 4, 2010

    As you must know there have been natural hybrids born in the wild. I believe you are completely incorrect in your statement that mutations are the cause of the differences between Polars and Grizzlies. If you can find this data I will stand corrected but my understanding is that the differences are more like a beagle and a great dane. All of the genes required for all dogs are present in the wolf genome. The various dogs were created by selective breeding focusing on certain traits(genes). Now the bears have far more variation since they separated 150-100,000 years ago but since they have fertile offspring they really are genetically amost identical.

  66. #66 Stuart Young
    December 4, 2010

    Yes I am quite familiar with VC funding since I have been involved with both public and private companies. Clearly private investment doesn’t chase rainbows but my point really was that over the past 50 years across the world there has been more than ample funding and time to pursue most of the promising ideas about origin of life. It is simply incorrect to state that lack of progress in origin of life research has been caused primarily by a lack of funding. Greg seems to assume that lack of complete agreement immediately suggests I’m a creationist or IDer. God plays no part in my analysis of the origin of life.

  67. #67 Stuart Young
    December 4, 2010

    Tulse-The value of owning the patents to the process that could create life from inorganic material would be very large indeed. If the process could be developed to create sustainable replicating life forms private industry would find many ways to create value.

  68. #68 Jim Thomerson
    December 4, 2010

    Well, from my point of view, how life originated is a grain of sand compared to considering relationships among modern species of fishes. We know that it originated. I don’t see any immediate technology applications of making new living things. Anyway I don’t have the background to make any meaningful contribution to how life originated.

    I understand the number of speculations, hypotheses, etc. are directly related to how poorly we understand something. As understanding increases, speculations and hypotheses do not survive, and are discarded.

    If we find living things out in the cosmos, and they have the same genetic code as living things on earth, I will then seriously consider panspermia.

  69. #69 Stephanie Z
    December 4, 2010

    Stuart, I’ll leave your understanding of population genetics to the experts, since that’s what you need to straighten you out (hint: it needs to incorporate mutation). However, I’d like to repeat Greg’s request for documentation of this “more than ample funding” you insist has existed. Who’s providing the funding? Where is it going? How much is ample for this purpose?

  70. #70 Stuart Young
    December 4, 2010

    Stephanie-Mutations have been the basis of explaining natural selection for many years but that is not proof that it is true. It also seems like the best explanation to me since it is the only plausible idea. However surely you know that almost every mutation is deleterious and Greg in his post claimed that the differences between polars and grizzies is the result of mutational changes. This is a big statement that I believe is completely unproven and instead the differences are the result of genetic variations being amplified by 150,000 years of separation. I’m sure you know that a Chiuaua is genetically a wolf. All the dog breed variations have occured without a single known mutation. In fact the experience in fruit flies mutations has not been productive in creating a new species of fruit fly. Despite these problems I still think it’s the best explanation since there are no better ideas.

  71. #71 Stephanie Z
    December 4, 2010

    So what you’re really saying, Stuart, is that you don’t have any documentation of major funding or research on abiogenesis?

  72. #72 Stuart Young
    December 4, 2010

    The study of the origin of life is not a new pursuit. Are you really claiming that the lack of understanding and advancement are the result of a lack of funding for over 50 years. The is one of the holy grails in science with a sure Nobel waiting for anyone who can create even the simplest one cell organism from inorganic compounds.

  73. #73 Brian
    December 4, 2010

    “The value of owning the patents to the process that could create life from inorganic material would be very large indeed.”

    It has already been done. Scientists have created organic matter from inorganic since the 1952 Miller-Urey experiments (and it was quite easy, life could spring from organic soup, not inorganic soup. Scientists can already create genetic information out of raw materials and the amount they can do is constantly increasing. They can already create synthetic life.

    Replicating the process that originally turned non-life into life on earth would be of scientific interest. However, we can already copy evolved life from scratch and even intelligently design life (and leave it to evolve later), we don’t need to restart evolution by duplicating the origins of Earth’s life. I’m not sure what the commercial value of that would be, especially compared to wholesale construction of designed multi-cellular organisms.

  74. #74 Brian
    December 4, 2010

    Sorry, what I said above wasn’t clear. A process exists for creating life from inorganic matter, however, it does not track Earth’s history of how that happened. That removes the commercial incentive, though. It also shows that the solution, if found, will be some physical process as in general physical processes certainly can do the trick. There is no difference in kind between this unknown (how exactly life arose on Earth) and other scientific unknowns.

  75. #75 Stephanie Z
    December 4, 2010

    So what you’re really saying, Stuart, is that you don’t have any documentation of major funding or research on abiogenesis?

  76. #76 Stuart Young
    December 4, 2010

    Stephanie-http://www.synbioproject.org/process/assets/files/6420/_draft/final_synbio_funding_web.pdf

    By the way do you believe in natural selection? If the answer is yes then most of your IQ blogs are wrong. Science ahd clearly proven that intelligence is genetically transmitted. There is no way to doubt this and believe in natural selection. The genetic tranmission is imperfect but the studies always show it amounts to somewhere between 50-70% of intelligence. You may not like the book the Bell Curve but most of the data in the back has been shown to be accurate by numerous independent studies. Arguing that intelligence isn’t transmitted genetically is about as silly as arguing that 6’5″ dads aren’t more likely to have children over 6′ feet tall compared to dads that are 5’7″. Now some short dads will have tall children and some tall dads will have shorter children but overall there is no rational debate.

  77. #77 Sarbo
    December 4, 2010

    Darwin had no theories about the origin of life. Origin of species was his signal contribution, along with others like Wallace. To say that species originated fron a “primordial” source says nothing about where and how that primordial source arose in the first place.

    Western science on the origin of life, here, there, or anywhere is mostly bunkum. Fat bureaucrats at the Encyclopaedia Brittanica in the 19th Century first talked of how an inorganic broth in the oceans was sparked by lightning into an organic broth, which in time formed cells and locomotion and reproductivity and sentient beings. Later, others had theories about life being brought to Earth by comets. Pure bunkum.

    As for life existing in an arsenic environment rather than phosphorus or carbon is underwhelming. We already know of life forms thriving in a sulphur environment, around volcanic vents on the ocean floor, right here on Earth. Big deal. When you discover how inorganic matter came alive, call me.

  78. #78 Stephanie Z
    December 4, 2010

    Stuart, you might want to look at the definition of “synthetic biology” before suggesting it has anything to do with abiogenesis.

    You might also want to actually read what I’ve written about IQ, as well as what Greg has. You wouldn’t have used either heritability estimates or “independent” research.

  79. #79 Stephanie Z
    December 4, 2010

    Sarbo, why would you go right back to the content of Stuart’s first comment and ignore everything that’s been said in between?

  80. #80 Brian
    December 4, 2010

    “Are you really claiming that the lack of understanding and advancement are the result of a lack of funding for over 50 years.”

    That depends. How old are you?

  81. #81 Sarbo
    December 4, 2010

    Stephanie, you ask “Why”. I had no idea I was referring to any comments. I was only reacting to the article and its basic underpinnings. Darwin was a deeply religious man. After he returned from his voyages, he wrote up his findings and his theories and then stored the papers in a drawer in his study for decades. He only published when he read about another naturalogist having similar theories. You should go back and read Darwin’s original notes. He was clearly staying away from second-guessing God’s mind. You may or may not believe in God but Darwin clearly did. He wrote of the descent of species and not the origin of life.

    People should leave Darwin alone. They might have various theories about the origin of life. Fair enough and I give them the respect they deserve. Just leave Darwin alone.

  82. #82 Greg Laden
    December 4, 2010

    Stu: “I believe you are completely incorrect in your statement that mutations are the cause of the differences between Polars and Grizzlies. ”

    I did not say that. Given that the differences we are talking about are clearly adaptations (white fur, adaptations related to swimming in freezing water, etc. etc.) the differences are caused by Natural Selection. Natural selection works on genetic variation that comes from mutations and drift, but ultimately from mutation.

    All of the genes required for all dogs are present in the wolf genome. The various dogs were created by selective breeding focusing on certain traits(genes).

    Yes indeed. See, here’s what you are missing: Selection is reduction in variation. Variation emerges ultimately from mutation but in addition from drift (which is a set of different things, but happening at the population level). The great diversity of allelic variation in both brown bears and wolves is due to mutation … that is how you get novel genetic material. No other way in diploid sexually reproducing animal types. Then, to get a Kodiak bear, a polar bear, etc. from brown bears or a beagle from a wolf, you select (well, you or nature).

    I think, though, that I may be missing your point. Or, you may be not getting what mutation is. I’m not sure.

  83. #83 Greg Laden
    December 5, 2010

    Clearly private investment doesn’t chase rainbows but my point really was that over the past 50 years across the world there has been more than ample funding and time to pursue most of the promising ideas about origin of life. It is simply incorrect to state that lack of progress in origin of life research has been caused primarily by a lack of funding

    Well, you can certainly take steps to prove your point instead of just saying it over and over again. I’m looking at two things, both of which I’m reasonably familiar with: 1) How much OOL research is represented in academia .. how many people mainly do this, how many departments shine in it, how many research centers have been erected to pursue it, etc. And, I’m looking at how much peer reviewed research there is in it. Of the several thousand peer reviewed research papers that come out every week, how many are OOL. My observation is that there is little academic commitment and very few papers.

    You are saying that there is a lot. Show us the beef. Do a literature search annd get the number of papers per year published in four or five main areas of biology, for comparison, and OOL research. Just produce some data to support the assertion you’ve come to the table with.

  84. #84 Greg Laden
    December 5, 2010

    Stu: Stephanie-Mutations have been the basis of explaining natural selection for many years but that is not proof that it is true.

    You need to stop insisting that you are not a creationist, because you are totally using the creationist playbook.

    Mutations have NEVER been the basis of explaining natural selection EVER. Where are you getting your information?

  85. #85 Jolene
    December 5, 2010

    “By the way do you believe in natural selection? If the answer is yes then most of your IQ blogs are wrong. Science ahd clearly proven that intelligence is genetically transmitted. ”

    Yeah, and we can see who fell in the shallow end of the gene pool, can’t we?

  86. #86 Stuart Young
    December 5, 2010

    Greg you clearly stated in your post that some of the variations between Polar and Gizzly Bears were due to mutations. This is simply not true any more than any dog breed is the result of mutations. I know the theory of mutations and how it relates to the theory of natural selection and I mostly believe it myself. However in this case the differences between the bears(color,webbed toes, claw shape, and organ differences) are not caused by mutations. The DNA of the bears has been studied and the genes responsible for these traits are also present in Grizzlies. If you reported that mutations are responsible for these changes it would be a major scientific paper since this has never been shown before. Now let’s be clear I’m not saying there hasn’t been a single mutation in polar bears in 150,000 years but that such a random mutation did not lead to the differences between the bears. There have always been light colored Gizzlies etc. The discussion about mutations is not a minor point. Are you still claiming that the differences between the bears has anything to do with random mutations? As for the quanitity of OOL research my point was that the paucity of published research is not caused primarily by a lack of funding but rather the complexity of the subject matter.

    Brian- The Miller-Urey experiments have been widely discredited over the years and are no longer accepted. Also inserting minimally changed existing DNA is a far cry from creating organic life from inorganic material.

    Stephanie- The research is closely related. Here is the intro.

    The Synthetic Biology Project was established in August 2008 at the Woodrow Wilson International Center for Scholars. The Project aims to foster informed public and policy discourse concerning the advancement of synthetic biology – an emerging interdisciplinary field that uses advanced science and engineering to make or re-design living organisms, such as bacteria, so that they can carry out specific functions. Synthetic biology involves making new genetic code, also known as DNA, which does not already exist in nature

    I believe engineering to make living organisms would qualify.

  87. #87 Greg Laden
    December 5, 2010

    Stuart,

    If if actually paid attention to what others were saying, you would make less of a fool of yourself by telling them (incorrectly) what they mean and then disagreeing with it.

  88. #88 Stuart Young
    December 5, 2010

    Jolene-Is this just a personal attack or are you arguing that intelligence is not substantially transmitted genetically. I know this is politically incorrect but the science in this area is not contraversial among those who study this field.

  89. #89 Stuart Young
    December 5, 2010

    Why do all of you find the need to add personal attacks to the posts? Greg is it your belief that the differences between the bears is or is not based on random mutations? In previous posts you seemed to make this claim.

  90. #90 Stuart Young
    December 5, 2010

    If on the other hand you are saying that mutations in the ancient bears caused genetic variation that was then selected by the polar environment then we agree. But again the mutations are an unproven theory that have never been shown in real life to benefit an organism(but it’s the only reasonable idea). But going from a grizzly to a polar bear is the child’s play of evolution compared to origin of life I spoke of in my original post. I takes no great insight to see how one gets from a gizzly to a polar bear. Origin of life is a different matter all together, yet all the textbooks(most recently my college age children) gloss over this and then spend most of the book explaining a far more simple process. If you publish a book with new insight, I will read this chapter with great interest. Can you send me a copy of the chapter?

  91. #91 Greg Laden
    December 5, 2010

    If on the other hand you are saying that mutations in the ancient bears caused genetic variation that was then selected by the polar environment then we agree.

    See? Paying attention is useful

    As one of those people who study the evolution and behavioral biology of human intelligence, I have to strongly disagree with you on the claim that intelligence is a genetic trait, though.

    But, I’m not sure you’re prepared for that argument, so I’ll just leave it there. Or here: http://tinyurl.com/2b9srnf

    Pay attention.

  92. #92 Sarbo
    December 5, 2010

    I’m sorry, but I can’t just leave this issue. People think they know what Darwin was about. He was mocked in his day. Even Huxley misunderstood Darwin. Darwin had a few facts from his Beagle voyages. Facts he did not invent. But he invented a theory, which he called “natural selection” to explain these facts. He never claimed this was a theory like any other theory you could find in the Physics world. It could never be tested or peer-reviewed.

    What Huxley could not get was that Darwin was not just saying that natural selection was a tool for species to adapt to changing environments. It was also a trap. Mankind is unique, in that he is not adapted. He can live in any environment, with the help of technology, which he invented for this specific purpose. Life is not adapted. Arsenic, Sulphur, Carbon, Nitrogen … life takes all in its stride. There is a will power, a drive to live, that no environment can dictate.

    Life is not inorganic or organic. It uses these chemicals to grow itself.

  93. #93 Sarbo
    December 5, 2010

    Arsenic, Phosphorus, Carbon, Nitrogen … go look up your Periodic Table. They are all over the place. Except one thing … they are among the heavier elements. No wonder. You women … worry about iron deficiency in your blood.

  94. #94 Sarbo
    December 5, 2010

    Greg Laden, you wrote this article which has brought all the worms out of the woodwork. I absolutely agree that intelligence is not inherited. Who is Einstein’s son? Nobody.

    But tell us what is mutation. A neutrino comes off deep space and hits ohomosomes … hey presto, we have a new species?

  95. #95 iş bul
    December 5, 2010

    If on the other hand you are saying that mutations in the ancient bears caused genetic variation that was then selected by the polar environment then we agree. But again the mutations are an unproven theory that have never been shown in real life to benefit an organism(but it’s the only reasonable idea). But going from a grizzly to a polar bear is the child’s play of evolution compared to origin of life I spoke of in my original post. I takes no great insight to see how one gets from a gizzly to a polar bear. Origin of life is a different matter all together, yet all the textbooks(most recently my college age children) gloss over this and then spend most of the book explaining a far more simple process. If you publish a book with new insight, I will read this chapter with great interest. Can you send me a copy of the chapter?

  96. #96 niewiap
    December 5, 2010

    Am I the only one to notice that NASA’s “Arsenic in DNA” data is highly suspicious? If you look closely at figure S2, you will notice that the average As content of DNA in bacteria cultured on pure As diet compared to pure P diet only goes up 2-fold – from close to nothing to a little less close to nothing. On the other hand the P content of DNA goes down 2-fold , which means that they are probably picking up some non-DNA molecules that contain high C:P/As ratio (the minuscule increase in As couldn’t possibly make up for a large amount of lost P). Maybe I misunderstand their methodology, but I think that they are full of it.

  97. #97 Stephanie Z
    December 5, 2010

    Stuart, you didn’t read the definition, did you? The research referred to in the pdf you posted is on manipulation of an existing genome or genomes to produce new varieties of life. It has nothing to do with how organic atoms came together to form self-replicating life.

  98. #98 Sarbo
    December 5, 2010

    I am quite amazed at the scientific illiteracy in these pages. NASA mined soil from a California lake and cultured it in a Petri dish and found arsenic. Big deal. I am from India. My ancestors came from what is now Bangladesh. In 75% of its districts, drinking water pumped from the ground is arsenic laced. They have adapted. No arsenic death epidemic, like AIDS. Humans live with bacteria in their tummies which would kill a cat. I know of some snake-handlers who survive a cobra bite without any anti-venom.

    Get real. Life is fierce. It has a will.

  99. #99 Stephanie Z
    December 5, 2010

    Sarbo, finding arsenic generally in bacteria isn’t what this is about at all.

  100. #100 Sarbo
    December 5, 2010

    The “mutation theory” has nothing to do with the “natural selection” theory. Mutation is instant. Natural selection takes millenia. One has to do with neutrinos from outer space, the other with environment here on Earth. Neither of which is proven.

    Let me just remind all you armchair scientists. Science has three clear stages. First, there is a Hypothesis. Then, there is a Theory. Finally, the hypothsis and the theory is a proven fact. There is no short cut.

  101. #101 Sarbo
    December 5, 2010

    So,Stephanie ,tell us what this is all about.

  102. #102 Greg Laden
    December 5, 2010

    Sarbo, Mutations are the primary source of genetic variation. Natural selection is one of the forces that reduces genetic variation.

  103. #103 Tulse
    December 5, 2010

    Mutation is instant. [...] has to do with neutrinos from outer space

    It’s a toss-up as to whether you’re more ignorant of biology or basic physics.

  104. #104 Stephanie Z
    December 5, 2010

    Sarbo, read the post if you want to understand the findings. Short version, however, is that arsenic was found in concentrations that the authors suggest mean the arsenic has to be in particular structures where it was previously thought arsenic couldn’t be used.

    Once you’ve read the post you’re commenting on, in detail so you know what it actually says both about this experiment and about the relevance for Darwin’s theories, perhaps you should go look up “theory” as used in a scientific context. It doesn’t have the meaning you’re trying to assign it.

  105. #105 darwinsdog
    December 5, 2010

    Mutation is instant. Natural selection takes millenia.

    Selective death occurs to individuals, Sarbo. Dying seldom takes millenia. Of course, most individual deaths are random, i.e., not selective. It takes surprisingly few selective deaths per generation for a powerful selective vector to arise & be maintained over evolutionary time.

    First, there is a Hypothesis. Then, there is a Theory. Finally, the hypothsis and the theory is a proven fact.

    The way it works is that a hypothesis is stated in null terms, and a test (experiment) of the hypothesis is conducted. The test either falsifies the null hypothesis or fails to falsify it. If further tests likewise fail to falsify the null hypothesis the hypothesis is said to be supported, but never proven. Science never “proves” anything; the best it can do is offer strong experimental support for a given hypothesis.

    I’m disappointed Sarbo. I really thought that the level of science education in India is better than you demonstrate.

  106. #106 billnut
    December 5, 2010

    “There may even be non-Darwinian life forms that arose in a certain pattern and never changed thereafter. ”

    But wouldn’t they arise by natural selection? Or are you saying they may be “special creations”.

  107. #107 Greg Laden
    December 5, 2010

    billnut: I don’t want to use the term “special creation” because that’s quite loaded.

    Here is what I’m asking us to (consider) imagining: Take the definitions we usually use of life: Self replicates, does certain things with energy, etc … so there is a thing that is found in a puddle or something that is unambiguously alive.

    But then, we find that the necessary and sufficient conditions for natural selection are not obtained in this organism. For some reason it’s replication is perfect, for instance, and there is no other source of variation. It would not evolve in a Darwinian sense. It may just be what it was, always. (But there may be other ways for variation to emerge)

    At the very least, it is possible to imagine life forms that are pretty much Darwinian but in ways that require some adjustment (like the vast majority of variation is introduced by some mechanism other than simple error).

    It is hard to imagine life without error, but it is easy to argue that we should not limit ourselves too much when making shit up about thinks we have not discovered yet. Until, of course, it becomes necessary to start parsing out research funds, then one needs to get a bit more pragmatic …

  108. #108 Stuart Young
    December 5, 2010

    Greg the data on the genetic inheritance of intelligence is beyond rational dispute. Like most people I find the subject difficult so I would probably not discuss it if I was a politician. However this is a science blog and if we can’t openly discuss a subject here then what is the point of the blog. At least two other posters have agreed with you and this is disturbing considering the many of you are recent graduates from elite schools. First of all even without the 60 years of data natural selection can not be true if IQ(imperfect measure) is not substantially inherited. So you with a Harvard Ph.d are going to tell me that the most important human trait is the only quality that is not based on genes. Even lay people are well aware that height, weight,running speed, eye color, etc. have major genetic components. If natural selection means anything in humans then 2-4 thousnd year of literacy, numbers, and civilization must select for slightly different genes in those population. The poster who believes that it’s evidence because Einstein’s son was not a genius simply doesn’t know the literature and science of genetic transmission of IQ. At any rate this topic is subject to extreme political correctness and I myself would normally not get into the details in general conversation. Avoiding the topic in polite conversation is one thing but claiming that IQ does not have a significant genetic component on a science blog is quite different.

  109. #109 Stuart Young
    December 5, 2010

    Stephanie you keep repeating yourself even after I pasted the exact wording from this big current research project. “To make or redesign living organisms”. Funding is tough for almost everything these days but some work is still getting done.

  110. #110 Stephanie Z
    December 5, 2010

    Stuart, it’s not repeating myself. It’s using slightly different words so you might have a chance of understanding. When they’re talking about making living organisms, they’re talking about taking parts from the genomes of already living organisms and rearranging them or combining them to make new organisms. They are starting with life, which means they are not studying how life arose from nonlife. They are not studying how DNA came to be from unorganized elements. They are not studying abiogenesis.

    Also, please explain why natural selection can’t be true if variations in intelligence aren’t genetic in origin? Currently, you’re merely asserting that as though it were fact. How much of the variation has to be accounted for by genes to validate natural selection?

  111. #111 darwinsdog
    December 5, 2010

    Greg the data on the genetic inheritance of intelligence is beyond rational dispute.

    Like any other continuous phenotypic trait, intelligence, as measured by IQ tests, is determined by both heredity & environment, and conforms to Fisher’s quantitative genetic equation. Estimates of the narrow sense heritability of intelligence, so defined, range from about .5 to .8.

    If we define intelligence as being “whatever an IQ test measures,” the heritability of intelligence is uncontroversial and quite high. Controversy arises when we consider that there may be more, perhaps much more, to what we’d care to include in a holistic definition of intelligence, than we know how to measure.

  112. #112 Stuart Young
    December 5, 2010

    Stephanie I’m remaining polite despite your attitude. I also have an advanced degree and really do understand this simple discussion. This research is very closely related as they are also trying to unlock nature’s secrets.

  113. #113 darwinsdog
    December 5, 2010

    They are starting with life, which means they are not studying how life arose from nonlife.

    Wherever one draws the line between an abiotic chemical self-replicating system and “life,” is arbitrary.

    How much of the variation has to be accounted for by genes to validate natural selection?

    Considerably less than has been shown to be attributable to the genetic component. Heritability estimates ranging from .5 to .8 are quite high. What’s unfortunate is that IQ and fecundity are rather highly negatively correlated.

  114. #114 Stuart Young
    December 5, 2010

    Darwinsdog I agree completely and also realize that IQ is a crude tool. But all through academia one can find well known experts claiming there is absolutely no genetic component to IQ when all of the data says otherwise. Besides in normal life no one is fooled anyway.

  115. #115 Stuart Young
    December 5, 2010

    DWdog now you are talking about reverse natural selection which seems to be occurring in the first world for a variety of reasons.

  116. #117 darwinsdog
    December 5, 2010

    DWdog now you are talking about reverse natural selection..

    Reversals of selective vectors due to environmental changes is what preserves genetic diversity in populations. Overdominance is merely a minor mechanism.

    ..which seems to be occurring in the first world for a variety of reasons.

    When selection pressure is relaxed, selective deaths are reduced and less rigorously adapted individuals manage to reproduce. The fact that IQ & fecundity is strongly negatively correlated has implications that Fisher explored in the latter half of his 1930 classic text. Since IQ is normally distributed with a mean, median & mode arbitrarily set at 100, over time what occurs can be described as “IQ inflation.” In other words, what qualifies as an IQ of 100 today may be the equivalent of an IQ of 90 a few generations in the past. Eventually, we end up with the “idiocracies” we’re beginning to see materialize in the developed world.

  117. #118 SaiFaiGai
    December 5, 2010

    My presumption, until more compelling information is revelaed, is that the bacteria mutated many, many times in this arsenic-rich environment, and eventually, a bacterium survived. This bacterium that survived was then in a completely uncontested ecosystem, and has remained.
    If the cell structure is so similiar, absent to As – P substitution, I think that it is the most probably answer.
    If it looks to be a separate occurence of life, a line unrelated to the primordial, then we should be joyful.
    This would portend a universe in which life “springs into existance” more often than we may think, under a varying set of conditions than we had considered previously.
    At a minimum, a complete As – P replacement would tell us that the preconditions for life are more forgiving than we’d presumed.

  118. #119 Stephanie Z
    December 5, 2010

    Stuart, I don’t care whether you’re polite or not. You’re wrong, and you’re persistently wrong. Astrophysicists are “also trying to unlock nature’s secrets.” Pretty much all sciences are. That doesn’t mean they’re studying abiogenesis.

    darwinsdog, I don’t know where you’re getting your information on IQ, but you’ve got pretty much everything wrong. Know anything about the Flynn effect? It’s a name for a phenomenon that is exactly the opposite of what you claim is happening. People tested now score higher on old tests than current tests, not lower. Older tests are easier.

    You also appear to be unaware that studies that assign a percentage of heritability to genes do so by first deciding what percentage they want to assign to non-genetic factors. Whatever is left over, they claim is genetic by default. That’s it. It may be accepted among the group of people who continue to do these studies (largely funded the Pioneer Fund), but that makes it neither generally accepted nor scientific.

  119. #120 Greg Laden
    December 5, 2010

    Stuart: Greg the data on the genetic inheritance of intelligence is beyond rational dispute. Like most people I find the subject difficult so I would probably not discuss it if I was a politician. However this is a science blog and if we can’t openly discuss a subject here then what is the point of the blog.

    Stuart, did you just tell me that my blog has a specific role, that you’ve determined, and if I do not meet that role, than there is no point in continuing? Did you also just say that the role of genes in intelligence is an issue that we do not need to discuss because it is settled in favor of variation in intelligence being determined by genes?

    Did you read the posts that I linked to above? You should probably go over them first, one by one, and make specific comments there.

    Joris, yes, I saw that.

  120. #121 Stuart Young
    December 5, 2010

    Stephanie in previous posts elsewhere you have clearly stated that you have a social science background. This blog is not the place for a detailed discussion about the study of the genetics of intelligence. I also suspect that Dwdog knows this data in much greater detail than me. Suffice it to say that the data(including very long term longitudinal studies) have shown that IQ has a significant genetic component. They have even isolated some of the genes recently that are linked to intelligence and found large differences of these genes between populations. Are you serious when you ask why intelligence must have a genetic component for natural selection to be true in humans? If this isn’t true what does natural selection mean for humans?Why did modern man out compete Neanderthal? Many people seem unaware that the teachings of anthropolgy over the past 50 years is wrong. We clearly know now that as recently as 25,000 years ago three distinctly separate members of the homo genus lived on the earth. The hobbit man appears to have lived as recently as 8,000 years ago. At any rate the data on the heritability of IQ is widely available.

  121. #122 Stuart Young
    December 5, 2010

    Top understand the importance of small differences in intelligence I think it helps to read in detail about the pleistocene ice age. Imagine the harshness of a world where 22,000 years ago an ice sheet 2-3 miles thick came all the way down to Manhattan. In fact most of the Statue of Liberty(except the torch) would have been under the ice. In this world very small advances in tools/weapons would mean a great deal in reproductve success.

  122. #123 Greg Laden
    December 5, 2010

    I think it helps to read in detail about the pleistocene ice age.

    Interesting. I’ll have to look into that.

  123. #124 Stuart Young
    December 5, 2010

    Greg you are a highly educated scientist so you know all this. But I live in a high end area and I’m always surprised at party filled with highly educated successful people how little most know about such things. In the recent past I suffered through a discussion/argument about global warming where neither side even knew the vaguest details about the laurentide ice sheet yet were cock sure they had all the answers. And amazingly the main protaganists in the argument both had MD/Ph.D’s. At one point I asked them both about the Younger Dryas and got a blank stare from both.

  124. #125 Stephanie Z
    December 5, 2010

    Stuart, let’s just say a social science background beats the hell out of your Masters in engineering for discussing this sort of thing. I’m actually familiar with the literature on the topic. You’re not. Neither are you familiar with the history or criticism of much of the literature that was generated in order to support claims of genetic differences in intelligence between races. Nor can you even conceive of what a valid criticism would be.

    All you know is that there are studies that say what you want to be true. It’s very much like you not understanding that funding research into genetic manipulation isn’t the same thing as funding how random elements ended up as DNA.

    No, there have not been any genes that have been shown to explain variations in intelligence. There have been a few studies that have claimed such a link by going through the genes of their target population until they find one that (by chance, as would be expected if one looks at enough genes) lines up well enough for publication. However, attempts to replicate those studies in new samples have shown those results to be the statistical flukes that they are.

    If you’d both read and comprehended the links Greg gave you, you’d already know this.

  125. #126 Jim Thomerson
    December 5, 2010

    Darwinsdog’s comment on an inverse relationship between IQ and fecundity may well be correct. However, consider Simple Darwinian Fitness, which is not a measure of fecundity, but rather a measure of success in raising offspring to adulthood. Many years ago a colleague told me of a study which found that Simple Darwinian Fitness does correlate with IQ. Is there anything to this?

  126. #127 Stuart Young
    December 5, 2010

    Stephanie is always angry. I’m not an engineer and I have read the literature. I’m a biotech executive these days. I never brought up the word race not once. You are substituting ideology for science if you really believe all populations of humans are so similar. If you look at the top one hundred 100 meter times in history virtually every runner has ancestry from the same river valley in Africa. For better or worse genetics has a large effect on almost everything. I’m actually concerned this genetic knowledge will soon go too far and become a potential problem.

  127. #128 Jason Thibeault
    December 5, 2010

    Stuart@126: if Stephanie seems angry to you, it’s only because she’s explained, twice now, and Greg’s linked evidence showing, that when looking at a large amount of genes, in a large number of populations, something is going to hit by pure chance to be correlated. And when the studies are revisited, those same effects don’t show up.

    For a great example of exactly the sort of effect you’re looking at here when you see these studies that “claim genetic links”, look at this code over at my blog explaining how the Mars Effect, the supposed correlation between people born Mars-ascendant and sporting ability, could have been hit upon by pure chance. This is similar to what you’re seeing when you look at thousands of genes, as opposed to a dozen planets/celestial bodies.

    Get it yet?

  128. #129 Stephanie Z
    December 5, 2010

    I suppose that technically, a director of an engineering division isn’t currently an engineer, but the position generally requires a degree in engineering. I could be wrong, though. Maybe your undergrad is in engineering and your “advanced degree” is an MBA-equivalent? Either way, a company that sells automated imaging gadgets and process consulting is a biotech company in very much the same way that messing with genetics is studying abiogenesis. That is, it isn’t. (Next time you want to stalk someone, try to understand that you leave traces.)

    More importantly, the racing argument is also old and tired and has been discussed to death on this blog. Try looking it up. It also matters not at all whether you use the word “race” when spouting racist tropes, any more than it matters whether you say “god” when spouting creationist arguments.

  129. #130 Stuart Young
    December 5, 2010

    Stephanie do you like dogs? I had a great Shetland Sheepdog years ago. We got him at eight weeks from the local breeder. This dog had never seen a sheep or learned anything about herding from any other dog. Yet at my uncle’s ranch this dog knew instinctively knew how to herd sheep. I was very intrigued by this and wanted to understand how this was possible. Over the years I have overseen various animal studies at a major vet school and so I asked my vet friends about this. They referred me to the book I attached but the bottom line is that many/most dog behaviors are controlled by specific genes. The breeders actually breed the border collie for this trait. The point is that dogs are not contraversial so no one gets offended. But the science of genetics is the same in humans as for dogs. I have no desire to offend anyone but almost every thing has a strong genetic component. There is no need to argue because in our lifetimes much of this is going to be understood in complete detail. But as I said this has a big downside as well. Would you want to know you have the gene/genes that predispose you to develop a fatal disease at an early age?

    http://www.dogwise.com/Item_Inside.cfm?ID=dtb551&curImage=2

  130. #131 Brian
    December 6, 2010

    “The Miller-Urey experiments have been widely discredited over the years and are no longer accepted. Also inserting minimally changed existing DNA is a far cry from creating organic life from inorganic material.”

    Think of a scientific experiment that has been validated and not discredited. OK, did that experiment show how life originated? No? Then it is discredited!

    Clearly, the above is ridiculous: experiments have to be interpreted. The ones in question have been duplicated and modified successfully. The only thing invalid are some interpretations, such as: this shows how organic molecules originated. That would be invalid since we do not know what the atmosphere etc. was like all throughout early Earth. One valid interpretation is the following: with 1950′s technology and a few days, it was not hard to get organic matter from inorganic matter. This invalidates your claim that the whole process from inorganic matter to life is a mysterious challenge to science. In the path from inorganic matter to dog, the sequence from inorganic to organic is more similar in how mysterious it is to the transition from wolf to dog than the transition from organic matter to life.

    “DWdog now you are talking about reverse natural selection which seems to be occurring in the first world for a variety of reasons…In this world very small advances in tools/weapons would mean a great deal in reproductve success.”

    Reverse selection makes no sense as a concept, it’s like reverse racism. Also, large brains have survival costs: they take energy, kill mothers in childbirth (by necessitating large heads, not through psychokenesis), etc.

    “…natural selection can not be true if IQ(imperfect measure) is not substantially inherited.”

    Why?

    In fact most of the Statue of Liberty(except the torch) would have been under the ice.”

    You Maniacs! You blew it up! Ah, damn you! God damn you all to hell!

  131. #132 SocraticGadfly
    December 6, 2010

    Back to the original theme of this blog post.

    Greg, it’s kind of clear this wasn’t just fluffery, but the arsenic experiment was poorly constructed in the extreme and therefore qualifies as “bad science.”

    http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html

    Therefore, I ask you again (and sit down, Stephanie) – What’s your motive in defending NASA’s fluffery, and now, what’s clearly worse than fluffery?

  132. #133 Sarbo
    December 6, 2010

    Somebody in these pages talked of “null nypothesis” and questioned India’s scientific talent. I just wish to say you can’t build a plausible (i.e. testable) null without having a plausible hypo to start with.

    As for Greg, mutations can’t possibly be the main vehicle of genetic differences. Otherwise, why would a giraffe be a close cousin of a sheep?

  133. #134 Stephanie Z
    December 6, 2010

    Really, Gadfly, you’re going to tell me to shut up? Try to be something less of an ass. And Greg already answered your question. You have yet to answer mine. Is it too terribly inconvenient for you amid all the frothing?

  134. #135 Stephanie Z
    December 6, 2010

    Stuart, why do insist on continuing to argue about things you know nothing about? Herding is a variation on pack hunting behavior, which is common to all dog breeds. Also, trying to argue that instinct tells us anything about intelligence is just silly when human brain development is nearly the antithesis of instinct.

  135. #136 Jason Thibeault
    December 6, 2010

    Sarbo @131: Giraffes are a close cousin to sheep? Well, I suppose by comparison between you and a nematode… but I fail to see how this cannot be accounted for by allele mutations and natural selection. What exactly is your proffered better explanation for the diversity of life, if not natural selection shaping populations’ allele frequencies?

    I have a post sitting in moderation that should go between 126 and 127. Serves me right for blog self-pimping, I guess.

  136. #137 Greg Laden
    December 6, 2010

    Jim: Many years ago a colleague told me of a study which found that Simple Darwinian Fitness does correlate with IQ. Is there anything to this?

    I’ve never heard of that study.

  137. #138 Greg Laden
    December 6, 2010

    As for Greg, mutations can’t possibly be the main vehicle of genetic differences. Otherwise, why would a giraffe be a close cousin of a sheep?

    BOING!!! flop flop floppity flop flop.

    That was my brain flying across the room and skittering across the floor.

    Jason: Sorry, the internet here (and apparently across large areas of the Twin Cities for Comcast users) was down for a long time. Comment freed.

  138. #139 Sarbo
    December 6, 2010

    Jason, you don’t think giraffes are related to sheep? Go back to the reasons you think humans are related to chimps. You count molecules like an arithmetic fact. I am not Marxist, but I think he, along with Darwin, had a thing or two to say about environment. Life can exist in any environment. Why don’t you address this?

  139. #140 Sarbo
    December 6, 2010

    I don’t much mind Jason’s views. He’s an illirate. But, you , greg. You are different. Are giraffes different from sheep? Put your hand on your heart or else you risk being classified with East Anglia scientists on climate.

    Tell us, Greg. Are giraffes anymore different from sheep than humans are from chimps?

  140. #141 darwinsdog
    December 6, 2010

    Reverse selection makes no sense as a concept..

    Selective vectors can change direction & magnitude and even reverse, as environmental conditions change. For example, two alleles coding for allozymes that differ in temperature or pH optima can have their frequencies shifted relative to one another as climate or hydrogen ion environment changes. One allele may be tending towards fixation while the other slowly goes extinct, until conditions change and the situation is reversed. If environmental conditions were constant much of the observed genetic diversity in populations would be eliminated. But since conditions change before beneficial alleles can become fixed and deleterious alleles go extinct, diversity is preserved.

    I don’t much care for terms such as “devolution” or “reverse evolution,” as commonly applied, but since selective vectors can and do shift & reverse I don’t see why you think that “reverse selection makes no sense as a concept.”

  141. #142 Greg Laden
    December 6, 2010

    “I don’t much mind Jason’s views. He’s an illirate.”

    I think this might have to be my facebook status for a while.

  142. #143 Greg Laden
    December 6, 2010

    Sarbo: “Tell us, Greg. Are giraffes anymore different from sheep than humans are from chimps?”

    What do you mean by “different”

  143. #144 Jason Thibeault
    December 6, 2010

    It’s on my own Twitter feed now, Greg. Which posts to Facebook. Badge of honour, frankly! :D

    Sarbo: what part of my comment, exactly, said that giraffes and sheep are NOT related? And why don’t you answer the question I asked: what hypothesis do you proffer that explains the diversity of life BETTER than natural selection and genetic mutation?

  144. #145 Brian
    December 6, 2010

    “…since selective vectors can and do shift & reverse I don’t see why you think that “reverse selection makes no sense as a concept.”

    Define selection and ask yourself if that word alone, without “reverse”, describes what is happening after the selective vector reverses. (The answer is “yes”).

    If you want to use “reverse selection” as selection after conditions change so that selection favors the opposite thing it did before, that’s fine and would be accurate but potentially misleading. In fact that may be the technical definition, but I think Stuart used it to mean something different. He doesn’t mean a description of the latter part of a sequence in which selective vectors have reversed, but rather selection favoring the inferior as such.

    Darwinsdog and Stuart said:

    “…What’s unfortunate is that IQ and fecundity are rather highly negatively correlated.”

    “…DWdog now you are talking about reverse natural selection which seems to be occurring in the first world for a variety of reasons.”

    “…In other words, what qualifies as an IQ of 100 today may be the equivalent of an IQ of 90 a few generations in the past. Eventually, we end up with the “idiocracies” we’re beginning to see materialize in the developed world.”

    This is part of a narrative in which human genes significantly affect intelligence and populations reproducing at higher rates in the West have less aptitude, and is in general an apocalyptic vision in which “reverse selection” means more than just that (supposedly) the environment selects for low IQ and no longer selects for high. It’s being used to mean selection of the worst/least intelligent, implying that true natural selection would be of the best, which is wrong because fitness is actually defined as success passing on genes relative to others, and not quality as an individual, power or intelligence.

  145. #146 darwinsdog
    December 6, 2010

    Define selection and ask yourself if that word alone, without “reverse”, describes what is happening after the selective vector reverses. (The answer is “yes”).

    Yes, selection is occurring regardless of what “direction” it is occurring in. But relative to the direction it was trending before the environment changed, it now may well be occurring in the opposite or “reverse” direction. “Reverse” is only meaningful relative to some former trend and is meaningless if only present conditions are being considered.

    I think Stuart used it to mean something different. He doesn’t mean a description of the latter part of a sequence in which selective vectors have reversed, but rather selection favoring the inferior as such.

    Okay, you may be correct. I apply no normative or pejorative connotation to the term, and use it only to selective vectors that have radically changed direction &/or magnitude due to environmental changes.

    ..”reverse selection” means more than just that (supposedly) the environment selects for low IQ and no longer selects for high.

    I wouldn’t claim that the environment actively selects for lower IQ but would say, rather, that selection for intelligence has been relaxed in the developed world, allowing people with lower IQs to enjoy greater fitness than they would have in the environment of ancestral adaptation.

    ..fitness is actually defined as success passing on genes relative to others, and not quality as an individual, power or intelligence.

    Of course. Once again, I don’t contend that the negative correlation between IQ & fecundity is due to selection, but to the relaxation of selection in modern society, rather.

  146. #147 Greg Laden
    December 6, 2010

    I wouldn’t claim that the environment actively selects for lower IQ but would say, rather, that selection for intelligence has been relaxed in the developed world, allowing people with lower IQs to enjoy greater fitness than they would have in the environment of ancestral adaptation.

    I think that phenomenon is real, but how do you tell the difference between selection on the cultural mechanisms of transmission of intelligence and the genetic ones?

    We have a lot of evidence of cultural transmission and as far as we can tell, that is how most or all stuff that manifests in the human brain gets passed on. We have no evidence that has sustained scrutiny for genetic transmission of such things.

    The world is divided into three groups of people: Those who are sure, with no advanced knowledge whatsoever, that intelligence and other important human traits are passed on through genes; those who are sure it is passed on through culture, and those who have not considered the question. Ignoring the third category, decades after this debate started to develop in its modern form (the early 20th century) no genetic basis for variation in intelligence (outside of people with, essentially, a broken CNS) has been found, but those in the first category continue to insist that it is true. They cite papers that cite papers that cite papers that have been discredited. Normally, in science, discrediting a basic finding propegates to question or force the re-evaluation of or the simple tossing out of findings based on that research that is now known to be incorrect. But in the field of IQ genetics, that never happens, and you get the sort of thing we are seeing in this thread, above.

    Meanwhile those who have felt that the vast majority of variation among humans with respect to our behavior and our brains is caused by non-genetic factors including cultural transmission have largely walked away from the fight because it is, frankly frustrating fighting with idealogs who insist that THEY are the real scientists and that those who don’t agree with their discredited theories are not being true scientists. Plus, by now we really do understand that the major feature of the human brain and of human development is the heavy reliance on that which is transmitted or developed extrasomatically. Our extended, costly, delicate period of neural development … utterly and astoundingly unprecedented among mammals … is there for a reason. It does what genes can not do.

    The real question is not genetics and intelligence … that is settled and need not be discussed at any length here. The real question is why there are still people who insist on this. What is their motivation? What are they getting out of this? I have found that a disproportionate number of individuals pushing the gene-IQ link are mentally ill in, usually, pretty similar ways, i.e., delusional and paranoid and obsessive, with the last of those three usually dominating. So, getting this question of biological and social sciences so utterly wrong often seems like a modern culture-bound psychiatric illness. For others, it is just plain racism. Often there is a mix of the two. But I’m speculating here. Nonetheless, that, rather than the issue of IQ and genes itself, is the real question at hand.

  147. #148 Jim Thomerson
    December 6, 2010

    When population growth rate increases, this suggests lowered selective pressure. Good times, in which individuals can have higher fitness than they would have had in hard times. In other words, the population becomes more variable in good times than in hard times. I am fairly nearsighted, corrected with glasses. In early times, I might not have survived to adulthood as a result. As it it is, I have raised three offspring to adulthood and thus have pretty good Simple Darwinian Fitness.

    The probability of life originating in the universe is p = 1. Probability of life originating more than once is unknown.

    Why is it called a “normal” distribution?

  148. #149 darwinsdog
    December 6, 2010

    The world is divided into three groups of people: Those who are sure, with no advanced knowledge whatsoever, that intelligence and other important human traits are passed on through genes; those who are sure it is passed on through culture, and those who have not considered the question.

    There is a fourth group: Those who have taken graduate level courses in quantitative genetics.

    Continuous phenotypical traits are determined by a genetic component + an environmental component + a nonadditive genetic x environmental interaction component + a dominance component. There’s probably an epistatic component too, but this is less rigorously resolved. The genetic component typically consists of a dozen or so genes of major effect along with hundreds of modifiers. Theoretically, these components are measurable, by means of twin studies, comparison with the midparental value, etc., and the equation can be rearranged to solve for the unknown component of interest. This is the way it’s done, or was done in the days before QTL mapping anyway, and human intelligence is an example of a continuously variable trait amenable to such analysis.

    Denial of all components contributing to individual human intelligence besides the environmental component strikes me as some weird Lockean philosophical throwback. I in no sense mean to denigrate the importance of environmental influences on quantitative traits but in the case of human intelligence, with a measured heritability (a metric of the proportion of the phenotypical variance that is genetically determined) ranging between .5 & .8, this happens to be a trait whose environmental determinants are relatively rather weak.

    For others, it is just plain racism.

    I don’t consider humans to possess a population structure that would render the concept of discrete human races even meaningful. For the concept of race to apply to humans, populations would necessarily have to group similarly regardless of whatever phenotypical trait was being used as the grouping criterion. This is not the case. Choose a given trait and you will get a grouping different from what results when some other trait is chosen. There are three races of Gorilla gorilla (four if you consider the Cross River population to be racially distinct from the Western Lowland population) but only one human race.

  149. #150 Stephanie Z
    December 6, 2010

    darwinsdog, given comment #119, why would you bring up that .5-.8 stat again as though it had any validity?

  150. #151 darwinsdog
    December 6, 2010

    Post#148: Concurred.

    Why is it called a “normal” distribution?

    Whenever someone says something to the effect of “What’s normal, anyway”? I love to reply, “It’s when mean, median & mode share the same value.” :)

  151. #152 Jason Thibeault
    December 6, 2010

    Darwinsdog@149: so the fourth group is those possessing advanced knowledge, but not advanced enough to rightly throw out specious data after it’s shown to be specious?

  152. #153 Greg Laden
    December 6, 2010

    There is a fourth group: Those who have taken graduate level courses in quantitative genetics.

    And there are those of us who have taught graduate courses in this.

    There are a lot of ‘traits’ that would have a ‘measured heritability very similar to either what you describe or what one might see in any of a wide range of human mental capacities and behaviors, but with variation that is, in fact not genetic. If you observe a phenomenon and assume a strong genetic basis, because there is evidence of such a basis, then the heritability metrics are useful. But applying the metrics and getting a result is meaningless. Language and language related traits, for instance, or tested knowledge of world culture and art, or civics. These will all follow these patterns.

    In the few tests that have been done where children of different supposedly IQ-distinct races were raised in a way that would maximize similarity via cultural processes all the children tested about 100 or so on IQ regardless of the color of their skin or the continent of their origin. In studies done of causes of IQ differences factors other than race dominant. If genetics or race has an effect, and there could be one, it is very very small and not yet detected. Why is it not detected? Because human beings have evolved this incredibly adaptable system of being called culture, which relies on this whopping big brain that can’t possibly be programed in any detail by genes, which produces results (and variations in results) that we in fact see.

    I can measure the objects in the junk drawer in my kitchen and apply plylogenetic computational methods to those objects using those measurements and obtain a valid phylogenetic tree showing which objects are more closely related to each other, and how they cluster into various taxonomic groups.

    But they are not organisms that have a phylogenetic relationship to each other. Well, most of them, anyway.

    If all you have is a hammer, the whole world looks a lot like a nail. If you firmly believe a priori that genes have a powerful influence on intelligence, I promise that you will see it in the data.

    I love to reply, “It’s when mean, median & mode share the same value.” :)

    What were you taking graduate courses in again? Because that is not correct. Close but no cigar, I would take away your gold star if you said this in my gradaute stats class.

  153. #154 darwinsdog
    December 6, 2010

    In studies done of causes of IQ differences factors other than race dominant.

    What’s with all this “race” rhetoric? There’s no such thing as discrete human “races.” Seems like you keep attempting to subvert discussions of the genetic contribution to intelligence and its heritability back to “race.” Homo doesn’t even have a population structure that makes the concept of “race” mean anything. Seems to me like you’re hung up in some late 20th century Gould & Herrnstein “race” thing. This isn’t about “race.” It’s about the simple fact that gene expression regulates the ontogeny of the human CNS that processes the concept we label “intelligence,” as modified by maternal effects and later learning. No one argues that environmental influences aren’t significant to the establishment of synaptic connections in the brain. The fact remains that overall neural architecture is largely genetically prescribed. The emphasis you seem to insist upon attributing to “race” places the onus of ideological bias on you. I’m only interested in biology here, not on cultural constructs such as unsupportable racial distinctions.

    I can measure the objects in the junk drawer in my kitchen and apply plylogenetic (sic) computational methods to those objects..

    This would be a phenetic rather than a phylogenetic analysis of said objects. That you confuse these methodologies makes me skeptical that you actually possess the expertise you imply.

    What were you taking graduate courses in again? Because that is not correct. Close but no cigar, I would take away your gold star if you said this in my gradaute stats class.

    The snark you would like to have yourself be thought notorious for only detracts from your credibility, Greg. Surely you can keep the dialogue on a more adult level than this. “..no cigar..” ” “..gold star..” Cliche much? Have you been drinking tonight?

  154. #155 Greg Laden
    December 6, 2010

    I appreciate that you don’t like the race concept, and that’s good. Usually IQ and race are interchangeable in these discussions, and though you chose one phrase I used, you’ve ignored the others in which I refer to genes, or “genes or race”

    Is your quote mining a form of subversion, or shall we just drop that insulting theme right here and now. The discussion of a major genetic component to intelligence is subverted by the lack of evidence for it.

    The fact remains that overall neural architecture is largely genetically prescribed. and doesn’t vary.

    No one argues that environmental influences aren’t significant to the establishment of synaptic connections in the brain. which is where the rubber meets the road when it comes to things like intelligence.

    The emphasis you seem to insist upon attributing to “race” places the onus of ideological bias on you. I’m only interested in biology here, not on cultural constructs such as unsupportable racial distinctions.

    Actually I’m pretty sure you are mainly interested in waving about this toy monkey to distract from the fact that you’ve pretty much got it wrong.

    This would be a phenetic rather than a phylogenetic analysis of said objects. That you confuse these methodologies makes me skeptical that you actually possess the expertise you imply.

    Are you being this stupid because you are stupid or because you are being willfully ignorant?

    Let me explain it again one more time (and this will be the last comment on this). Please read this really slow so it does not go whizzing by this time, because I’m a busy and this conversation is quickly becoming a waste of time.

    If I were to treat a bunch of objects using PHYLOGENETIC TECHNIQUES then I would get PHYLOGENETIC TREES even though that would be the WRONG METHOD. It would still give me results. When you apply the techniques you allegedly learned in what must have been a piss poor graduate seminar on genetics to things that are not genetic, you still get results. Very rarely do techniques like this (and this is a general problem in methodology) tell you that you somehow that they are being used inappropriately.

    If you tested for heritabilty of Trait X by looking for it in grandparents, parents, children you might find that there is a high degree of H. But if Trait X is language … say, language one speaks, lexicon one uses, grammatical constructs one tends to build on, etc., H would be high. But it isn’t genetic. Are you getting this?

    The snark you would like to have yourself be thought notorious for only detracts from your credibility, Greg. Surely you can keep the dialogue on a more adult level than this. “..no cigar..” ” “..gold star..” Cliche much? Have you been drinking tonight?

    You’re gone. Apologies by email might or might not be accepted.

  155. #156 Tom S.
    December 6, 2010

    You’re gone.

    Thank you. I have run into this self aggrandizing twit elsewhere on the Internet, and he won’t back down or let up, so it is nice to see it end. IIRC he is also an AGW denier. I have noticed the persistent gap between knowledge and self identification with Darwin or some other great intellect to be very common.

  156. #157 Jason Thibeault
    December 6, 2010

    Ahahaha! “Surely we can keep the discourse civil, you clichee-spouting alcoholic.” Just too precious.

  157. #158 Greg Laden
    December 6, 2010

    The funny thing is, I did screw up by conflating race and genetics in this discussion, partly because I dismissed dog’s reference to race as a ploy (we see that a lot) but also just because I’ve been taking care of my infant son and have been rather distracted while addressing his comments.

    Or was I busy sinking into an alcoholic daze? Can’t remember which one. Six of one, half dozen of the other. Water under the bridge, really. Pot calling the kettle black, I suppose.

  158. #159 billnut
    December 9, 2010

    Greg. I just don’t see how you get something that is “unambiguously alive” without some natural process that would qualify as evolution.

    You said, “At the very least, it is possible to imagine life forms that are pretty much Darwinian but in ways that require some adjustment (like the vast majority of variation is introduced by some mechanism other than simple error).”

    But natural selection can work on any type of variation, from simple error to designed interventions. I have actually designed lab strains to use in selection experiments. If Darwin did say it had to be “simple error” (and I don’t think he did) then that’s just one more reason to stick to science and natural selection and stop cultivating this cult of Darwin.

    ” but it is easy to argue that we should not limit ourselves too much when making shit up about thinks we have not discovered yet.”

    That’s religion, you’re arguing for the god of the gaps.

  159. #160 Greg Laden
    December 9, 2010

    Greg. I just don’t see how you get something that is “unambiguously alive” without some natural process that would qualify as evolution.

    Yeah, it’s hard. I’m proposing that we think about the possibility that an organism can exist that is not generally subject to Darwinian Natural Selection (not evolution, but natural selection) or at least that most variation in the type of organism can’t be explained with reference to NS. It may well be impossible.

    But natural selection can work on any type of variation, from simple error to designed interventions.

    Yes it can, and it is only because we have no such variation in organic systems that the agreed upon definitions of NS become tricky. The three necessary and sufficient conditions for natural selection to occur ( http://tinyurl.com/2eh5wxe )include things other than selection, but may include things that would not be present or primary in this hypothetical type of life I’m thinking of.

    I have actually designed lab strains to use in selection experiments.

    That’s artificial selection, of course.

    Darwin didn’t say “simple error” as far as I know, that was me. And, as far as I know, the fast majority of variation that works with NS comes from mutation, one base pair at a time, or relatively simple errors that cascade to other larger genomic differences (gene duplications, etc.). We can remove the word simple if you like, but that would be off the point.

    ” but it is easy to argue that we should not limit ourselves too much when making shit up about thinks we have not discovered yet.”

    That’s religion, you’re arguing for the god of the gaps.

    OK, you restrict your thinging (or, spelled correctly, thinking) to things that have already been thunk and call everything else religion. Meanwhile, hopefully, others will try to be imaginative and exploratory and think new thoughts and maybe discover new stuff.

    It does boggle my mind that you feel that I’m arguing for a god of the gaps here.

  160. #161 Jim Thomerson
    December 9, 2010

    Wallace parted company with Darwin on the question of the human brain as a result of natural selection. Wallace held the view, heretical at the time, that primitive tribal people were just as smart as upper class Englishmen. However, they lived such simple lives, that such intelligence was far beyond what was needed and thus could not be the result of selection.

    When I took cultural anthropology in 1955, the professor argued that a tribal shaman had just as much knowledge as an MD. I think anthropologists have embraced the idea of little intellectual variation among peoples, and argue against Wallace’s idea that anyone has a simple life not requiring high intellect.

  161. #162 Greg Laden
    December 9, 2010

    Jim, I think that’s pretty accurate.

    Boaz, Kroeber, Levi-Strauss and other key early anthropologists discovered the incredibly intricate and complex features of culture that the “natives” had well after Darin and Wallace.

  162. #163 billnut
    December 9, 2010

    “It does boggle my mind that you feel that I’m arguing for a god of the gaps here.”

    I guess I worded that poorly. You wrote,

    “we should not limit ourselves too much when making shit up about thinks we have not discovered yet.”

    My point is that when you say we can just make up shit to explain what we don’t know you are on the same intellectual level as the religious folks who just make up shit to explain what they don’t know. At the heart of the scientific method is the idea that you don’t just make shit up. You stand on the shoulders of those who came before you, to paraphrase one famous scientist.

    “OK, you restrict your thinging (or, spelled correctly, thinking) to things that have already been thunk and call everything else religion. Meanwhile, hopefully, others will try to be imaginative and exploratory and think new thoughts and maybe discover new stuff.”

    Well, you obviously don’t understand my point. I have spent decades studying this and discussing the origin and evolution of life with some of the best minds in the field. I have actually discovered gene duplications that created new enzymatic function. It is my knowledge of the subject that led to my objection to what you wrote. Disagree if you wish, I can take it. But there is no reason to belittle those who disagree with you, that’s not how good science is done.

    Let’s turn this positive. Articulate your alternative hypothesis for an evolutionary process that does no involve natural selection by your three criteira and we can discuss it.

  163. #164 Greg Laden
    December 9, 2010

    My point is that when you say we can just make up shit to explain what we don’t know you are on the same intellectual level as the religious folks who just make up shit to explain what they don’t know.

    Well, here, I’m putting some burden on my readers, I admit. I’m assuming that my readers would not think that I’d actually advocate that we do science by “making shit up” and see the humor in this phrase.

    I have spent decades studying this and discussing the origin and evolution of life with some of the best minds in the field. I have actually discovered gene duplications that created new enzymatic function. It is my knowledge of the subject that led to my objection to what you wrote.

    Good, I’m gladyou did that stuff.

    Disagree if you wish, I can take it. But there is no reason to belittle those who disagree with you, that’s not how good science is done.

    But you do need to stop this habit of yours of finding ways to tell me (and others) that you are the good scientist and I am not. It’s embarrassing.

    Let’s turn this positive. Articulate your alternative hypothesis for an evolutionary process that does no involve natural selection by your three criteira and we can discuss it.

    I did that already, at least to the extent I’m prepared to at the moment. Replication that is nearly perfect, and/or a system where by replicates that do not resemble the template are always destroyed.

  164. #165 billnut
    December 9, 2010

    “But you do need to stop this habit of yours of finding ways to tell me (and others) that you are the good scientist and I am not.”

    Come on Greg. I was responding to your assertion that I must somehow be unimaginative and restricting my thinking if I dare disagree with you. Accept that some folks just think you’re wrong once in a while. Try to understand why rather than resorting to insults. I never said you are not a good scientist, I don’t know your work. Personal attacks are never good science. I didn’t realize that you were just joking in the earlier post (nice retreat).

  165. #166 billnut
    December 9, 2010

    I asked you to articulate your alternative hypothesis for an evolutionary process that does not involve natural selection by your three criteria and we can discuss it.

    You responded, “I did that already, at least to the extent I’m prepared to at the moment. Replication that is nearly perfect, and/or a system where by replicates that do not resemble the template are always destroyed.

    But nearly perfect is not perfect so there are errors. Small variants do resemble the template. This is solid ‘Darwinian’ stuff. Your earlier response @107 said, “For some reason it’s replication is perfect, for instance” and talked about “life without error”. But now we know you were just joking.

  166. #167 Stephanie Z
    December 9, 2010

    billnut, this isn’t that hard to get. Greg was not joking in the meaning of his prior statement. He was, however, using a hyperbolic description of creativity (“making shit up”), trusting his readers to get it.

    You didn’t get it. You insulted him. Now you insist he can’t insult you. Thus, you’re insisting that your status is somehow greater than his.

    Get over it.

  167. #168 billnut
    December 9, 2010

    I really did not intend to insult anybody. I apologise if I did. I am not interested in “status”, I just believe he is in error on a scientific point of interest. That is not an insult. I just don’t think his scenario stands up to scrutiny.

    Trust me, I’m over it ;-)

  168. #169 Greg Laden
    December 9, 2010

    Come on Greg. I was responding to your assertion that I must somehow be unimaginative and restricting my thinking if I dare disagree with you.

    OK, fine. Sorry if I overreacted, that happens when the creationist accusation comes up. I know, as I’ve been on both sides of that one (but why bring up bad memories…)

    But nearly perfect is not perfect so there are errors. Small variants do resemble the template. This is solid ‘Darwinian’ stuff. Your earlier response @107 said, “For some reason it’s replication is perfect, for instance” and talked about “life without error”.

    WEll, I could have said (and did originally say) “perfect” then you would say (reasonably) “there is no such thing as perfect” and I would say “imperfection in copy making is widespread in our Earthly Darwinian system. It defines much of how it works. Every individual organisms with more than a few thousand genes has at least one copy mistake. So imagine a system where one individual in 100,000,000,000 has a small mistake, and one in 1,000,000,000 get past the mistake finding mechanism … ” and so on.

    But now we know you were just joking.

    Why do I get this impression that you’re not really trying to make this conversation work?

    If you like we can try it this way: A system of life in which copies are perfect. No joking. That would be one in which Darwinian natural selection would not be operative.

    But to skip back to the more realistic version in which about one error gets passed on every 500,000,000 years or so on a planet able to sustain life for 1,500,000,000 years (so you get three mutations ever) … We do say, pedantry aside, that the diversity of life we see on earth today, biologically, is primarily the result of Darwinian processes with Natural Selection as the key ‘creative’ force. Fine. Then we further define that system … there are genes with info passed on from generation to generation, sometimes imperfectly, thus drift/random variation, and then selection, bla bla bla. And we’re done with our description, and we go on with our research.

    But then there are ERVs and giardia (somatic mutations passed on to offspring), gene eating bacteria and endosymbionts, etc. etc. Turns out that there are a number of somewhat different systems that if they dominated, the above referenced description would be substantively different.

    In the world I’m imagining … the near perfect world, near is good enough. Replication is perfect and the effects of imperfection is the rare exception that scientists might even overlook for centuries of research rather than the modal case.

  169. #170 billnut
    December 9, 2010

    OK, sorry if the “special creation” was poking you in the eye. I just goggled you and I see why you reacted like that. We are on the same side in this one and that is why I reacted to your original statement with that phrase.
    Quite seriously, I do think your scenario gives ammunition to the creationist, however unintended. I can hear them twisting it around to show that you leave room for special creations and scientists just make shit up (OK, I won’t mention that again), or a least that Darwin was wrong on some level.
    Also, I don’t buy your scenario. How does this perfect life arise if not from modification of earlier forms? Start with a simple molecule that can catalyze its own formation from two other molecules. How do you get from there to something that is “unambiguously life” without imperfect copying? As soon as it is not perfect, natural selection applies. At best, an organism could evolve to become a perfect replicator, but then in all likelihood you have an evolutionary dead end in a changing environment, and environments always change.
    I’m not sure I get your point about somatic mutations, endosymbionts, etc. They are all raw material for natural selection. Natural selection encompasses much more than Darwin could have ever imagined. I don’t even think allelic variants is a term he would recognise. That’s why I don’t like the cult of Darwin. We don’t talk about Newtonian gravity or Plankian quantum mechanics, etc. If you do, you miss what came after those immensely important contributions to current knowledge.

  170. #171 Greg Laden
    December 9, 2010

    I just goggled you and I see why you reacted like that.

    Well, now I can sleep at night.

    Quite seriously, I do think your scenario gives ammunition to the creationist, however unintended.

    Well, it isn’t intended, but it also does not matter. I’m not inclined to censor myself to avoid creationists turning comments into ammunition. That may be a consideration very very rarely, but usually not. Their intention is not to get everyone to believe in their point of view. Their intention is to interfere with science because they see it as as powerful aspect of the secular society they fear. When my fellow rational scientists avoid using perfectly good descriptive language or terminology, for instance, to avoid this sort of thing, I cringe because every time that happens, a creationist somewhere sprouts wings, or gets to fuck a virgin, or whatever it is they tell themselves.

    And, when I first wrote that I was very well aware of the “Darwin was wrong” thing and I’m waiting to see that bit of bait tugged at. There will be consequences.

    As far as this conversation goes, you need to think this out more carefully than you’ve done. You are suggesting to me, and I appreciate the suggestion even though I don’t agree with it, that I should consider avoiding saying that there could hypothetically be an origin of life that would not involve Natural Selection, because Creationists will see this as a Darwin was Wrong thing and exploit it. But then you say “..That’s why I don’t like the cult of Darwin. …”

    Gee, thanks, man, you just relegated Darwin to a cult. The creationists are going to make hay with that one!!!!!

    Now, to a side point: “I’m not sure I get your point about somatic mutations, endosymbionts, etc. They are all raw material for natural selection.”

    This is not too important but I’ll address two aspect of this . First of all, somatic mutations, in standard modern evolutinoary thinking, have so little to do with Natural Selection that a) they are warned against in intro and intermediate texts and b) the are not addressed almost anywhere, and it would be trivially easy to construct a scenario to get most advanced researchers in Evolutionary Biology to slap you one if you mention somatic mutations as part of Darwinian processes. So no, a form of life in which somatic mutations were responsible for variation but the key replicator was perfect would require a different looking evolutionary biology with a different description of evolution and classic natural selection would be minor.

    Now, to the main point:

    “Also, I don’t buy your scenario. How does this perfect life arise if not from modification of earlier forms? Start with a simple molecule that can catalyze its own formation from two other molecules. How do you get from there to something that is “unambiguously life” without imperfect copying? ”

    Exactly. that’s why I said, explicitly, and you didn’t like this at the time because you thought I was a creationist, so go back and rethink why you don’t like this: It is going to take some imagination and creative thinking to come up with plausible scenarios for something we might call “life” that is fundamentally different, because all our thinking and experience is with what we consider run of the mill life and it’s few odd variants. Also, it may require violating one of the seven features (or whatever the current number is) that the textbooks use to describe what life is.

    What if there is a primordial soup with complex interactions involving polymers. Some of the polymers get washed, now and then, across a substrate containing semi crystalline rock (like mica or something) and when the right combination of polymers occurs together, you get a cell-like feature that uses photosynthesis to generate energy, and uses the energy to improve the substrate so the cell-like structures are more numerous, and the material infiltrates it, spreading over time. That’s a lot like life, no replication.

    Of course, I’m just making this shit up, as promised. The thing is, the assertion that it is impossible for there to be a form of natural activity that we would probably agree to be a form of life that has characteristics fundamentally different than what we are accustom to is kind of silly. It’s an unprovable/un-disprovable tautology.

    It may be that all life “elsewhere” or in some distant primordial Earthly past will look just like life does now … cells, D/RNA, proteins. Or that minus the proteins. Or, there may be very different things going on somewhere/somewhen. Assunming that there is nothing different, nothing unknown, is pretty much how a lot of the day to day bench science that happens (and engineering) gets done, but it is not how the occasional startling new idea comes up.

    At best, an organism could evolve to become a perfect replicator, but then in all likelihood you have an evolutionary dead end in a changing environment, and environments always change.

    One of the key characteristics of life on earth is that it adapts over time to changing environments. Here, you insist that is indubitably true of all possible forms of life in all other places and times. That would be a good example of what I’m talking about.

  171. #172 Jim Thomerson
    December 9, 2010

    Somatic mutations are fairly important in flowering plant variation. Remember that germ cell lines are not segregated in flowering plants as they are in most animals. It is not unusual to notice a limb of a bush or tree with different color flowers, or leaf shape. Here is an interesting paper on somatic mutation and predation.
    http://www.jstor.org/pss/2461561

  172. #173 billnut
    December 9, 2010

    Well, now I can sleep at night.

    Just can’t resist the sarcasm, eh?

    But then you say “..That’s why I don’t like the cult of Darwin. …” Gee, thanks, man, you just relegated Darwin to a cult. The creationists are going to make hay with that one!!!!!

    But I’m not the one trying to make a name for myself on the web as an evolutionary expert. I warn about the dangers of the ‘cult of Darwin’ because it is dangerous. It leads to the argument from authority fallacy. It is not about Darwin, it’s about biology.

    you didn’t like this at the time because you thought I was a creationist,

    Nope, I never thought that or said that. I put “special creation” in quotes in my response to a biologist to try to make a point.

    it would be trivially easy to construct a scenario to get most advanced researchers in Evolutionary Biology to slap you one if you mention somatic mutations as part of Darwinian processes.

    I would usually agree but you were the one @169 who brought up “somatic mutations passed on to offspring” so I went along to avoid dragging us off topic.

    So no, a form of life in which somatic mutations were responsible for variation but the key replicator was perfect would require a different looking evolutionary biology with a different description of evolution and classic natural selection would be minor.

    Not true. If they were passed on to offspring, as YOU specified, and were responsible for the variation underlying their evolution, then they would satisfy your three criteria that are necessary and sufficient for natural selection to occur
    1. Variation in a trait
    2. Heritability of the trait
    3. Differential fitness conferred by the trait.

    Now, to the main point:
    ….
    It is going to take some imagination and creative thinking to come up with plausible scenarios for something we might call “life” that is fundamentally different,
    ……
    Also, it may require violating one of the seven features (or whatever the current number is) that the textbooks use to describe what life is.
    …..
    That’s a lot like life, no replication.

    But you said “unambigously life”, not a lot like life, or something we might call life if we change the accepted definition(s) of life. @107 you said, “Here is what I’m asking us to (consider) imagining: Take the definitions we usually use of life: Self replicates, does certain things with energy, etc … so there is a thing that is found in a puddle or something that is unambiguously alive.

    You’re a slippery one Greg.

    The thing is, the assertion that it is impossible for there to s characteristics fundamentally different than what we are accustom to is kind of silly.

    I never said that. Stop changing your story and putting words in my mouth.

    Assunming that there is nothing different, nothing unknown, is pretty much how a lot of the day to day bench science that happens (and engineering) gets done

    Nonsense.

    I wrote, “At best, an organism could evolve to become a perfect replicator, but then in all likelihood you have an evolutionary dead end in a changing environment, and environments always change.”
    You responded, “Here, you insist that is indubitably true of all possible forms of life in all other places and times. That would be a good example of what I’m talking about.

    I suggested “in all likelihood” and you turned it into, “you insist that is indubitably true” to facilitate your personal attacks and avoid the issue in front of us. That’s a great example of what I’m talking about.

  173. #174 Christopher
    December 9, 2010

    OMG I have never seen anything so annoying.

  174. #175 Greg Laden
    December 9, 2010

    billnut: Well, you said the magic words.

    I will take all of your advice as to how to be a better person into consideration and get back to you on that. Meanwhile, I’m certain I’ve addressed all the concerns you raise in your most recent comment in earlier comments.

  175. #176 Synthetase
    December 10, 2010

    Forgive me if these points have been made already, but I haven’t the time to read all preceding 175 comments.

    Mr Laden, are we reading the same paper?

    “This [GFAJ-1] was placed in a medium that contained all the necessities of bacterial life, to allow the bacteria to be alive, to thrive, to grow, and to reproduce, except phosphorus. This soup also contained a high level of arsenic.”

    Sorry, but the background level of phosphate was ~3 uM, not zero. This is important because it undermines their assertions.

    “Thus the experiment. And it worked. Even in the absence of phosphorous, in an arsenic rich environment, a bacterium thrived. (This is an oversimplification, but that is the general idea.) When they looked more closely, they discovered that the arsenic had substituted for phosphorus in part of the DNA of the bacterium.”

    No, when they looked closely, they discovered that there was As present in their sample. They did not show that it was part of the DNA. Because their sample also contained DNA, they made the assumption that As had become part of it. This is wrong.

    If they wanted to show that there was indeed As in the molecule, they should have done X-ray diffraction to show the extra electron density of the DNA; or a variant of the Meselson-Stahl experiment which was performed in the 1950s using heavy Nitrogen 15 to show the semi-conservative replication of DNA.

    The other thing that gets me about this experiment is that there is only a two-fold difference between the ratio of As:C in the As+/P- cells versus those given P. This isn’t very high and is especially low if their hypothesis that the P starved cells are supposed to be incorporating As into the chromosome. Their description of sample preparation at this point is also vague and they could just be measuring the ratio of As to C in the gel.

    “The test of this hypothesis (a partial test, anyway) would be to reconstruct the phylogeny of this bacterium. Did it separate from the other bacterial lineages at a time near the origin of life, or much more recently? Wolfe-Simon and her team are at present not saying anything about the phylogeny of this bacterium, and when asked about it at the press conference indicated that they just don’t know yet.”

    This was in the paper! And I quote:
    “Currently this isolate, strain GFAJ-1 identified by 16S rRNA sequence phylogeny as a member of the Halomonadaceae family of Gammaproteobacteria”

    This family of bacteria contains such well-known pathogens as E. coli, Salmonella and Shigella. Clearly if their claims are true (and I see very little evidence to support them) this represents a (relative to the appearance of life and divergence of Bacteria from Archaea and Eukaryotes) recent separation.

    I was going to make a few other points, but they elude me at present. Suffice to say that the evidence supporting their claims is very thin. Some better controls would have served them well.

  176. #177 billnut
    December 13, 2010

    All life on earth descended from a single, original, primordial form that arose eons ago.

    With all due respect to Ernst Mayr and the keeper of this blog, that was not what Darwin believed. The last sentence in the “Origin” reads,

    “There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one … from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”

    Darwin never (to my knowledge) spent much time thinking about the origin of life, his great contribution was to suggest a mechanism, natural selection, to account for the evolution of the diversity of life and the creation of new species.

  177. #178 Greg Laden
    December 14, 2010

    The paragraph you cite is an interesting one. It is usually cited in relation to the addition of “A Creator” in later editions. Otherwise, it is a great example of how Darwin wrote everything.

    Darwin may or may not have been the first modern scientists, I personally think he was the first prominent one, in that he does something very consistently that other candidates for that label of the day did not do (and many do not do today in fact): Recognize the contingent nature of virtually everything. This is reflected in Darwin’s writing everywhere, and you’ve cited a good example of it.

    Ernst Mayr is a significant Darwin authority that I’ll trust in this case over “billnut.” All due respect and all. There is nothing I’ve read in Darwin that contradicts Mayr in this regard, and much that supports it. I’ve read most of what Darwin has written.

    The “Origin of Species” is about origins, and Darwin makes the claim that there is a common origin for all forms of life. Much of The Origin is about evidence for this. He discussed this elsewhere as well. The contemporary literature of the time notes again and again that Darwin accepts, consistently the common origin idea (it was not originally his but advanced by him). The fact that Darwin supported common origin is noted by Darwin in his notes of other people’s notes of him. It was his thing. It was central to his view of life, and it is the thing that blew his mind. It is the thing that he observed that drove him to find an explanation, and that explanation was adaptive evolution (Natural Selection). Darwin was Common Origin guy.

    But of course, when he gets to to the end of his book, being Darwin, he throws in the possibility that there is more than one origin. He does the same kind of thing with many of his other ideas as well. Annoying yet wonderful.

  178. #179 Greg Laden
    December 14, 2010

    I would like to add: It does not matter to Darwin if there are multiple origins, only that as far as he can tell all forms of life have common origins with other forms of life. He explicitly notes that the major forms of life (as they were thought of in that day) … plants and animals … internally have common origins (he cites numerous examples) and that plants and animals have a common origin (he provides evidence) and the “lower forms” (the things not plants and animals) may be different but probably also have a common origin (and cites his reasoning for this So he does demonstrate some equivocation but concludes that there is a common origin.

    But he maintains the mild equivocation of common origin in his final paragraph, and one wonders if there is a consideration of the key point I made above in this post when he says that.

  179. #180 Jim Thomerson
    December 14, 2010

    Comment in response to post #170. We routinely make many physical measurements in units named for famous folk, Einsteins, Newtons, Ohms, Volts, etc. etc. Have you ever heard of the Darwin, a measure of evolution? One Darwin is a 1% change in the genetic make up of a population? The term is not in general use so far as I have noticed. Sort of runs counter to the idea of a cult of Darwinism.

  180. #181 Irene
    December 14, 2010

    It is a secret cult.

  181. #182 billnut
    December 16, 2010

    Hi Greg,
    You may (or may not) be interested in listening to one minute of the following link, from 3:20 to 4:20. Dan Dennett, no intellectual slouch, does a much better job than I did of explaining my objection to your scenerio

  182. #183 Greg Laden
    December 16, 2010

    Well, first of all, that was not an argument, it was a statement of what we have to think when thinking about Darwinian evolution. I happen to agree with it, but it was not an argument.

    Second, that was a conversation about evolutionary models vs creationist models for explaining life on earth. This has nothing to do with my conjecture.

    Third, arguing that Dennet is somehow more correct in your mind than your view of what you are confused about what I’m saying is a piss poor and irrelevant counter argument (which I only suspect it to be but can’t be sure, though I’m probably right) from your spectacular bit of evidence by example that sometimes authority (Ernst Myer vs. BillNut) is a clue. Hey, you’ve got a pseudonym for a reason. Just change it. No one will know it’s you! :)

  183. #184 billnut
    December 16, 2010

    As for the comment on units, you are missing my point Jim. A Darwin as a unit of change in the genetic make up of a population is probably not in general use because it has not been a particularly useful unit of measure for most scientists. Modern genomics may change that.
    The cult comment comes from the habit of calling evolution a Darwinian process. It’s akin to calling electricity a Voltian process, but we don’t do that.
    Evolution is a natural process. Natural Selection, as proposed by Darwin, may be the greatest single idea in the history of humanity, but the field has grown beyond what Darwin could have envisioned. Mendel and Mieschner (sp?) both published their work within 10 years of Darwin’s publication of the Origin of Species. Their work came together decades later in the “Modern Synthesis”.
    As pointed out earlier, a strict ‘Darwinist’ would hold that life was “originally breathed by the Creator”. Most biologists have a different view, but we are not ‘Millerian’ or ‘Ureyian’ biologists.

  184. #185 Andrew
    December 16, 2010

    It’s akin to calling electricity a Voltian process, but we don’t do that.

    It is more akin to calling mechanics a Newtonian process. We do that.

  185. #186 papapound
    January 16, 2011

    But there does not have to be a culture war between theory of evolution and theories of creation.

    See here:
    http://goodnewsnow.wordpress.com/2011/01/16/origins-of-life-part-2/

  186. #187 Marta Torres
    August 2, 2011

    Sr Greg Laden, as I said by email, I wrote an article with this resume: Darwin’s evolution theory has as its first premise the conception of common ancestor, which means that all beings come from the same origin. This is confirmed by Neo-Darwinist theories that combine such information with the fact that all living beings are composed of DNA. However, through the discovery of a bacterium that has a composition different to that of all other living beings, therefore not having gone through the process of evolution, the first premise of Darwin can be considered erroneous. By applying the theory of deductive logic, this bacterium discovered would invalidate Darwin’s theory, and therefore the theories based on evolutionism, including the theory that applies fundamentals rights only to humans. Removing evolution as an irrefutable premise it is possible to break this legal paradigm, allowing us to rethink the anthropocentric conception of the application of fundamental rights and enabling us to extend them to other living beings as well as humans. Althought it’s written in portuguese, I show in my blog some Darwin’s quotes (in English), so you would understand why I think his theory BROKE DOWN. Thanks for your atention.
    http://manuaisdeinstrucao.blogspot.com/2011/08/como-defender-que-as-plantas-e-peixes.html

  187. #188 Marta Torres
    August 3, 2011

    DARWIN SAID: “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case. No doubt many organs exist of which we do not know the transitional grades, more especially if we look to much-isolated species, round which, according to my theory, there has been much extinction” (DARWIN, Charles. The origin of species. London: Collector’s Library, 2004, page 210).
    That’s why I think we need to think about the evolution theory, and it has nothing to do with religious matters, ’cause I’m also against the christian religiou’s anthropocentric point of view. I’m not a biologist, so you are the one who can tell me if the evolution theory survive after this bacteria.

  188. #189 NJ
    August 3, 2011

    Marta Torres @ 188:

    I’m not a biologist, so you are the one who can tell me if the evolution theory survive after this bacteria.

    I’m not a biologist either, but it easy to understand that it can without much problem.

    From the OP:

    But owing to some sort of brilliant insight, Wolf-Simon thought arsenic could sometimes substitute for Phosphorus, and she reasoned that the best place to find that biological difference would be in organisms that had evolved in a place where there was a LOT of arsenic, yet life still existed despite the presence of this nominal poison.

    Arsenic is highly toxic. But a very few organisms exposed to a high arsenic environment do not die because of some (in this case) advantageous mutation. Those organisms flourish in the arsenic environment because of a lack of competition, allowing for more mutations over time. Most of these are either neutral or harmful, but a few are helpful. Eventually, a mutation occurs that causes the organism to require arsenic to live and reproduce.

    Completely consistent with what we know about mutations and natural selection. What you need to do is learn a lot more biology before trying to rewrite a fundamental part of biology.

    Come back in, say, a dozen years.

  189. #190 Marta
    August 6, 2011

    If that “fundamental part of biology” is based in a wrong premise, it would take me not only 12 years but a lifetime learning wrong theories… Insted of this, I rather study logics and recomend all biologist to do the same, so they would reflect that if that bacteria is different from all beings alived, that evolution theory might be revisited.

  190. Biologists are forcing Darwin’s theory to a mutation, so it can be adapted to that new discovery and to the fact that there are virus which are also different from all other beings alived. Can we say that evolution theory is mutating so it can be adapted to the science natural selection?

    It didn’t take me 12 years to understand the fact that if a theory finds at least one thing to prove that one premisse is wrong, so that theory would break down(as Darwin himself said when talking about a discovery of an organ which was not part of the same process of evolution).

  191. #192 NJ
    August 6, 2011

    Marta @ 190:

    Insted of this, I rather study logics and recomend all biologist to do the same, so they would reflect that if that bacteria is different from all beings alived, that evolution theory might be revisited.

    Your grasp of modern biology and logic is, quite literally, at about the same level as your grasp of English grammar and spelling.

    Spend less time on the Internet and more time in a classroom.

  192. #193 Marta Torres @TorresMarta
    August 7, 2011

    You are right, I’m not american and although I’m trying real hard to speak perfectly your language I make lots of mistakes, but at least I’m trying to speak your language so we can talk about science(and not expecting you speak portuguese to do so). Sorry for my bad English grammar and spelling, but I think you can get my idea. Try to foccus on it, if you can.
    I do not spend time in the internet with stupid things, insted I invist my time reading blogs like yours so I can understand a little more about life. As I’ve already told you, I’m a lawyer, who is trying to understand the evolution theory ’cause it’s passed to the law students (like me) as a truth, but I do not think so. I’m here to discuss science, ’cause this evolution theory is applied to human rights’ theory to justify why only humans have the right to live (and this right cannot be applied to animals) – that’s what I’m researching in my masters.
    I think we can learn some things outside the classes, reading blogs like yours and the discussion it’s being developed. If you want all the students to stuck on a classroom to understand everything, you shouldn’t be writing a blog on the internet.
    I hope if you can’t respond my point of view about Darwin, at least you respect me as a student. We have a popular quote that says “no one knows so much that doesn’t have anything else to learn and no one knows so few things about life that doesn’t have anything to teach”.
    Again, sorry about my english mistakes. But I’m sure you are smart enough to get the idea.

  193. #194 @TorresMarta
    August 7, 2011

    You are right, I’m not american and although I’m trying real hard to speak perfectly your language I make lots of mistakes, but at least I’m trying to speak your language so we can talk about science(and not expecting you speak portuguese to do so). Sorry for my bad English grammar and spelling, but I think you can get my idea. Try to foccus on it, if you can.
    I do not spend time in the internet with stupid things, insted I invist my time reading blogs like yours so I can understand a little more about life. As I’ve already told you, I’m a lawyer, who is trying to understand the evolution theory ’cause it’s passed to the law students (like me) as a truth, but I do not think so. I’m here to discuss science, ’cause this evolution theory is applied to human rights’ theory to justify why only humans have the right to live (and this right cannot be applied to animals) – that’s what I’m researching in my masters.
    I think we can learn some things outside the classes, reading blogs like yours and the discussion it’s being developed. If you want all the students to stuck on a classroom to understand everything, you shouldn’t be writing a blog on the internet.
    I hope if you can’t respond my point of view about Darwin, at least you respect me as a student. We have a popular quote that says “no one knows so much that doesn’t have anything else to learn and no one knows so few things about life that doesn’t have anything to teach”.
    Again, sorry about my english mistakes. But I’m sure you are smart enough to get the idea.

  194. #195 Stephanie Z
    August 7, 2011

    Marta, all organisms are different from the other organisms alive on Earth. The fact that there is non-cellular life doesn’t invalidate evolution. Viruses still have plenty in common with plants, animals, etc. that points to a common ancestor. Also, I think you’re a bit confused about what this experiment actually says, even if replicated (which is looking doubtful these days). Read Greg’s post again in full.

  195. #196 Greg Laden
    August 7, 2011

    Maria: Darwin’s evolution theory has as its first premise the conception of common ancestor, which means that all beings come from the same origin.

    I think calling it a “first premise” is a post hoc thing you’ve added. Darwin never said that. If I were to infer a first premise from Darwinian Theories I’d say it was descent with modification.

  196. #197 Marta Torres @TorresMarta
    August 7, 2011

    Thanks Greg Laden and Stephanie Z. I think now you got my good intention with this discussion. I want to make it clear that I have nothing to do with all those religious speeches about creationism. As I said before, I think those speeches are also anthropocentric, and I’m not interested to ressurect that church idea of the begging of life.

    So I’ll quote now what Darwin said in his book:

    “In considering the origin of species, it is quite conceivable that a naturalist, reflecting on the mutual affinities of organic beings, on their embryological relations, their geographical distribution, geological succession, and other such facts, might come to the conclusion that each species had not been independently created, but had descended, like varieties, from other species. Nevertheless, such a conclusion, even if well founded, would be unsatisfactory, until it could be shown how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation which most justly excites our admiration. Naturalists continually refer to external conditions, such as climate, food, etc., as the only possible cause of variation. In one very limited sense, as we shall hereafter see, this may be true; but it is preposterous to attribute to mere external conditions, the structure, for instance, of the wood-pecker, with its feet, tail, beak and tongue, so admirably adapted to catch insects under the bark or trees.” (DARWIN, p. 11)

    “Now let us turn to nature. When a part has been in an extraordinary manner in any one species, compared with the other species of the same genus, we may conclude that this part has undergone an extraordinary amount of modification, since the period when the species branched off from the common progenitor of the genus. This period will seldom to be remote in any extreme degree, as species very rarely endure form more than one geological period.[…] And this, I am convinced, is the case. That the struggle between natural selection on the one hand, and the tendency to reversion and variability on the other hand, will in the course of time cease; and that the most abnormally developed organs may be made constant, I can see no reason to doubt.” (Darwin, p. 172-173)

    “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case. No doubt many organs exist of which we do not know the transitional grades, more especially if we look to much-isolated species, round which, according to my theory, there has been much extinction” (Darwin, p. 210).

    (DARWIN, Charles. The origin of species. London: Collector’s Library, 2004)

  197. #198 Collin
    September 14, 2011

    Wasn’t there something about bacteria that use tungsten instead of sulfur?

  198. #199 hoary puccoon
    September 14, 2011

    If, in some extreme environment, organisms are discovered that don’t stem from the same abiogenesis as the rest of us, evolutionary biologists won’t be upset that evolution has been “disproven.” They will be absolutely ecstatic!

    Two completely separate evolutionary lines would make it possible to test all kinds of hypotheses that can’t be tested now– because all known organisms are too closely related.

    People who think that evolution can be “disproven” by some minor, new discovery just don’t understand the huge weight of evidence supporting evolutionary theory. It’s not like sinking the Bismarck– it’s like sinking the whole continent of Europe.

    (Bom dia, Marta. :-) )

  199. #200 Richard Aberdeen
    May 3, 2012

    There are other reasons why life may be similar, other than single origination. Darwin himself allowed for multiple origins, as well as Darwin credited a Creator with being behind evolutionary processes, two well established facts ignored by most modern intellectuals.

    If life arrived on space rocks, as some scientists have proposed, then what arrived may have been quite similar or even identical, may have been “seeded” abundantly throughout the earth and thus, arose from all over the earth and, is so complexly cross-integrated at root levels, as to only appear to be singular in origin.

    Another perhaps more likely reality, is that what causes life to arise came out of the big bang, is refined in stars along with the majority of elements, is spread througout the Cosmos within zillions of planetary environments, as so much “fertilizer” waiting for conditions to arise favorable for it to “arise”. This life “fertilizer” may be identical or nearly identical in structure, which would also explain similarity of life, which may indeed have arisen all over our planet, from zillions of tiny identical or nearly identical life forms, as well as arisen abundantly throughout the Cosmos.

    More Information on why modern evolutionary theory is mainly a poorly contrived “human construct”, grossly inadequate to actual explain how, when, where or why life came to exist on our planet:
    http://freedomtracks.com/500/theory.html

  200. #201 Marta Torres
    Brazil
    June 9, 2012

    strange… where are the other comments?

  201. #202 Jim Brock
    Houston, Texas
    January 14, 2013

    Off topic, but: How do the thermal vent species fit into this discussion? Strange but similar beasties.

  202. #203 Greg Laden
    January 14, 2013

    I think it is believed that the symbolization, which are chemo-synthetic bacteria, come from more than one origin but they are basically bacteria that don’t use photosynthesis and have the ability to get their energy from a hydrogen pathway and using other chemicals (sulpher) at vents. They don’t use arsenate instead of phosphate for anything.