Apr 25 2014

Prebiotic Earth

One of the great scientific mysteries is the specific processes and pathways that led to the first living organisms on earth. This is not mysterious in that we don’t know how it could have happened, it’s just that it is extremely difficult to reconstruct how is actually did happen. Chemical reactions don’t fossilize, and so understanding a complex process that likely took millions of years to unfold billions of year ago is a bit challenging.

Researchers have mostly had to rely on plausibility studies – experiments that show how prebiotic evolution could have happened and extrapolating from data on early earth conditions. More progress has been made with this type of research. The title of the paper says it all – Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean. (Markus A. Keller, Alexandra V. Turchyn, Markus Ralser)

The researchers showed that, in conditions based upon published literature about the early prebiotic ocean, certain metabolic pathways central to life could happen spontaneously and without the presence of enzymes. That last bit is critical – enzymes are proteins that act as catalysts, which are substances that make a chemical reaction happen faster. Enzymes are critical to life, as the biochemical reactions of life would occur at too slow a rate without them.

Creationists are fond of making the “irreducible complexity” argument that life could not occur without enzymes, and enzymes are created by life, so how could such a system ever start? The basic answer is that without enzymes biochemical reactions are slow, but not nonexistent. They still occur. So prebiotic chemistry and even early life could have still used these reactions, but they would have been very slow and inefficient. Life could then simmer along and evolve the more sophisticated metabolic machinery we see today.

The current research demonstrates this principle. In fact, it demonstrates that metals, such as iron, under conditions likely to be present in the prebiotic ocean, would act as catalysts for certain metabolic pathways central to life, “glycolysis and pentose phosphate pathway-like reactions.” These critical reactions would occur at a functional rate without enzymes.

Further, the authors make a plausible argument based upon their findings that much of the basic metabolic pathways that make up living organisms could have been going on in the prebiotic oceans without life. In other words, metabolism itself predates the first life. The early oceans could have been “primordial soups” of chemical reactions, creating many of the building blocks of life.

Their research is also compatible with other research showing that primitive RNA was plausibly the earliest replicating molecule.

While we currently do not have the ability to peer back into time and see what was actually happening on earth 4 billion years ago, scientists have painted a fairly compelling picture of at least the broad brushstrokes of how life could have arisen. The early oceans had all the ingredients of life. These ingredients spontaneously form into the building blocks of life. RNA can arise spontaneously, and make copies of itself, setting into motion the potential for chemical evolution. And now we also can see that the metabolic reactions of life could have been humming along in the oceans of early earth before life arose.

Now all we need is for bubbles of bilipid membranes to spontaneously occur, which they do, encasing RNA, the metabolic soup, and amino acids and other building blocks of living cells. We don’t quite have a living cell yet, but we have a plausible precursor to a cell. Another point that creationists often miss is that scientists do not claim that a modern cell came together spontaneously, just the raw ingredients. From this point we still need hundreds of millions of years to evolve the complex machinery of a modern living cell.

It still seems amazing that the machinery of life could bootstrap itself into existence in this way. How did RNA learn to direct the synthesis of proteins, for example? That was a huge step in developing life’s machinery. I predict future research will shed further light on this process, like showing how such direction could occur spontaneously, although very slowly and crudely.

That is all you need, however. Once RNA has the tiniest toehold on the direction of protein synthesis, we are off to the evolutionary races. That creates an evolutionary feedback loop – RNA essentially catalyze and direct the creation of proteins from amino acids, and these proteins help the RNA do just that, as well as replicate itself, and then take over catalysis of the biochemical reactions that are already happening, create surface proteins to affect the internal environment of the evolving cell, proteins to help direct and control activity within the cell, and then more and more sophisticated protein structures.

Every tiny incremental step would have been a huge evolutionary advantage. There is no irreducible complexity here – we have pieces of the puzzle all the way back to spontaneous prebiotic reactions. We don’t have all the pieces to the puzzle, not even close, but we have enough to say that there is no irreducible complexity to the metabolism of life.

77 responses so far

77 Responses to “Prebiotic Earth”

  1. grabulaon 25 Apr 2014 at 8:01 am

    The timing on this article is fortuitous. I’ve been going back and forth with my boss who’s a firm creationist. He keeps sending me links to articles on creation.com and not being well read in this area I’ve done some scrambling to understand the issues they raise.

  2. grabulaon 25 Apr 2014 at 8:04 am

    I meant to add that what I am discovering is that since science has yet to come up with a solid theory – though we’re getting closer all the time – that abiogenesis is viewed as the weak link not only to itself but to evolution as well. I see my boss moving in that direction with our discussion – mostly over email since we work different shifts. It’s weird to me that these people seem to forget that prior to any theory being backed up by robust data, science still has to look for the theory to test in the first place.

  3. RickKon 25 Apr 2014 at 10:51 am


    I’ve had this debate quite often. Obviously, use caution when debating the boss 🙂

    One key point in debates like this: “supernatural intelligent agents” (God, spirits, demons, etc.) have been proposed throughout history to explain natural phenomena. Yet every mystery of nature we’ve ever actually solved turned out to NOT be the result of such agents. With such dismal prior probabilities in mind, when explaining an as yet unanswered mystery of nature, ALL burden of proof is on the person claiming supernatural agency. Because “God did it” has been proved wrong repeatedly and never proved right, the person using that argument must first provide extraordinarily solid evidence of the existence and capabilities of God.

    That said, here are a few things we can say about abiogenesis:

    1) All life on Earth (that we’ve studied) shows characteristics completely consistent with common descent. This is true along multiple lines of evidence.

    2) That original common progenitor did not appear suddenly in a burst of biochemical magic/luck – it was in turn the result of earlier evolutionary processes (replication with variation guided by reproductive success).

    3) As Steve points out, self-replicating molecules that are not “alive” can “evolve” to be better replicators, so we know evolution can happen to “pre-life” molecules.

    4) The simple ancestors of modern life weren’t made out of just anything, they were made out of chemicals that just happen to be generated by plausible abiotic mechanisms found in the early solar system.

    5) The exact point between non-life and life was likely as fuzzy and indistinct as the dividing line between Latin speakers and the first French speaker.

    6) If indeed the first life was formed by intervention by a highly advanced or supernatural entity, the entity went to great lengths to stretch the process out over a long period of time and to create massive amounts of evidence to make the result look like it formed through natural processes.

    Finally, the lack of a solid answer on abiogenesis is NOT a weakness of biological evolution. Are the laws and rules of chemistry dependent upon knowing where the elements came from? Species evolve from earlier species with no apparent divine intervention. This is proved beyond reasonable doubt. Saying “evolution may not be true because we don’t know how it started” is the same as saying “physics may not be true because we don’t know how it started”.

    A nice collection of origin of life research can be found here: http://stonesnbones.blogspot.com/2008/12/origin-of-life-outline.html

    Good luck! And always remember Steve’s approach – first find common ground, then build on that. Don’t expect to change your opponent’s mind – the best you can expect to do is give him some irrefutably rational arguments on which to dwell.

  4. weegreenblobbieon 25 Apr 2014 at 4:20 pm

    One more point to make, that has been repeated on this blog many times before. The god of the gaps came from somewhere. How did this super-natural being come into existence? Was it created magically too? By whom then?

    Saying “god did it,” does not answer the question since it only shifts the question to where did god come from.

  5. grabulaon 25 Apr 2014 at 10:01 pm


    Thanks for the advice, some of it I’ve touched upon, some of it is helping me look in other directions. Of course I don’t really think he will change his mind, I think in fact his only goal is to change mine.’

    Really, the only point I wanted to hit home with in our discussion was the fact that a major and important difference between creationist and scientists is that scientist adapt to the science as it develops while creationist try to twist the science to adapt to their world view. Once you attempt to really remain intellectually honest, the bottom falls out of the arguments against things such as evolution from a creationist standpoint.

  6. Double Helixon 26 Apr 2014 at 7:02 am


    Great post. I remember watching Cosmos (the first one) when Sagan showed the experiment in the glass container filled with “early Earth” gases and sparked with artificial lightning.
    Stunningly, for me, he showed that the building-block molecules of life were produced, over time, by this simple and plausible process. This revelation had a huge impact on me, when I realized that we humans were coming closer and closer to figuring out the origins of life.

    Sagan was a profound influence on the direction my life has taken since then. Although I had been out of high school for years, I decided to go back to school. You might say that Sagan got me my Physics degree!

    I don’t think that it is an exaggeration to say that Dr. Steven Novella is rapidly rising to the stature of recognition of Dr. Carl Sagan. You are already one of the “go-to” guys among skeptics, and you are on many media rolodexes. I hope that, within a decade or two, you will also be a household name, like Sagan. You deserve it!

  7. tmac57on 26 Apr 2014 at 11:11 am

    Does anyone doubt that if and when we conclusively show how life came from natural processes,that believers will (if they don’t just reject the evidence outright) say “That just shows HOW God did it,not that he didn’t do it”.
    Those goalposts can be moved infinitely.

  8. sonicon 26 Apr 2014 at 12:37 pm

    I have difficulties with the points you make (I don’t think they are as true as you seem to).
    Would you be willing to discuss this?

  9. Paulzon 26 Apr 2014 at 5:14 pm

    You’re a lucky man to have a boss who’s willing to have a friendly discussion, Grabula.

    This is fantastic news for the difficult and contentious subject of abiogenesis. Of course, it won’t really do anything but move the goalposts back for Creationists – but maybe it’ll sway a few more of them, bit by bit.

  10. BBBlueon 26 Apr 2014 at 11:06 pm


    I’ve been going back and forth with my boss who’s a firm creationist.

    If a person is willing to accept a literal interpretation of the bible as evidence, then I don’t think there is any point in engaging that person in a science-based discussion on the origins of life unless they approach you out of a genuine curiosity and desire to understand a different point of view. To many people, the fact that science does not explain everything is a very unsatisfying proposition; for them, it is better to believe in a fiction than to leave questions unanswered. Sometimes, you just have to know when to disengage and talk about sports and the weather instead. Perhaps it is more important to investigate and better understand the issues for your own education rather than attempt to educate others.

  11. etatroon 27 Apr 2014 at 4:41 am

    Second tmac. If the premise is that a divine, all powerful creator made the universe including life, and we discover means of a chemical origin for biological processes, then it follows that the means were put in place by the creator, it created the means. The long time frame is the extend of its plan (which is only seemingly long given our perception of time which is influenced by our lifespans). It goes on as far as the mind which presumes the creator is willing to take it. I see no way to refute creationism if a creator’s intervention is considered to be self evident.

  12. RickKon 27 Apr 2014 at 3:42 pm


    Sure – happy to discuss.

    What are your difficulties?

  13. BillyJoe7on 27 Apr 2014 at 6:00 pm


    Except that said creationist will object to the multiverse on the basis of waste of time and space, even though no extra concepts are involved.


    Good luck.
    Make sure he sticks to HIS difficulties, not the difficulties of people he quotes and links to and with whom he may or may not agree without explicitly saying so. (;

  14. Davdoodleson 28 Apr 2014 at 4:17 am

    @Etatro: “If the premise is that a divine, all powerful creator made the universe including life, and we discover means of a chemical origin for biological processes, then [theists will inevitably argue that] it follows that the means were put in place by the creator, it created the means.”

    Yep. However, as Carl Sagan wrote in Broca’s Brain:

    “As we learn more and more about the universe, there seems less and less for God to do…. When Newton explained the motion of the planets by the universal theory of gravitation, it no longer was necessary for angels to push and pummel the planets about. When Pierre Simon, the Marquis de Laplace, proposed to explain the origin of the solar system–although not the origin of matter–in terms of physical laws as well, even the necessity for a god involved in the origins of things seemed profoundly challenged.”

    I think that the religious are not just ‘moving the goalposts’ (which they are), but that, as scientific knowlege increases, they are inevitably moving the goalposts further away, into ever-smaller ‘gaps’, the shadows and crevices of superstitious, bronze age wonder. ‘God’ may exist, but science is showing with more and more certainty that God’s not doing anything that is distiguishable from what we would observe if it did nothing. Or if it had never existed.

    If religion is “the opiate of the masses”, science has diluted it to homeopathic concentrations.

  15. Bill Openthalton 28 Apr 2014 at 6:39 am

    DavDoodles —

    If religion is “the opiate of the masses”, science has diluted it to homeopathic concentrations.

    And then succussed it to make it even more potent :).

    How else does one explain it continues to attract people?

  16. sonicon 28 Apr 2014 at 11:32 am

    My problems with your statements have two aspects-
    1) are they relevant
    2) are they exaggerated

    The question is ‘How did life begin?’

    Is ‘common descent’ relevant? Without knowing how life began, I’m not sure how one would distinguish between ‘common descent’ and ‘common design’, so I’m not sure it’s relevant.
    Are the evidences for ‘common descent’ exaggerated? I would say so.

    Your point #2 is called ‘begging the question’.

    Point #3- I don’t think this has been demonstrated in any meaningful way- can you give me an example?

    Point #4- This is another form of ‘begging the question’.
    Take a look at Pasteur’s experiment– all the ‘building blocks’ of life are available– but life will not arise without the introduction of life itself.

    Point #5- So now we can say that we don’t know how what we can’t define came into being. I’m not sure this is a good argument for abiogenesis.

    Point #6- Huh?

    I agree that ‘evolution’ and ‘abiogenesis’ are different subjects.
    One is about the starting point (abiogenesis), the other is about what happens given a starting point.
    I’m not sure how well either are understood-

  17. steve12on 28 Apr 2014 at 1:01 pm


    “I’m not sure how one would distinguish between ‘common descent’ and ‘common design’”

    Give the evidence, this is a ridiculous thing to say.

    “Are the evidences for ‘common descent’ exaggerated? I would say so.”

    Agan, absurd. Almost nothing in science has as much convergent evidence. Even the link you provide doesn’t agree with you! Nothing in that link questions a tree structure formed by common descent. There’s a huge difference between understanding exactly what the tree looks like and knowing there’s a tree. That article talks about uncertainty in the former but certainly not the latter.

    I know you want to be seen as having daring opinions. My advice to you is to try something less settled than this. INstead of daring you look reflexively contrarian.

  18. Steven Novellaon 28 Apr 2014 at 2:17 pm

    There are absolutely ways to distinguish common descent and common design. The molecular evidence is most compelling: http://www.talkorigins.org/faqs/comdesc/section4.html

    Examination of amino acid sequence redundancy, base pair sequences, and transposons all show a nestled hierarchy of relationships among living organisms consistent with common descent. There is absolutely no reason for this pattern due to common design – unless it is your hypothesis that the desinger designed life to look as if it were the result of common descent, which is both nonsensical and unfalsifiable.

    Common design does not explain the fossil record, the distribution of species, details of developmental biology, biochemical pathways, and anatomical quirks that only make sense within the common descent theory.

    The point of #2 is that scientist do not hypothesize a sudden appearance of life, but a slow evolution from prebiotic precursors, so when creationists debunk the “sudden appearance” idea they are attacking a straw man.

    You entirely miss the point of #4 – Life is made out of material that was abundant and spontaneously occuring in a plausible early Earth. If life were created, it could have been created out of stuff that does not just occur spontaneously.

    #5 – again, you miss the point. Life from non-life does not require some huge leap or fundamental change in the nature of stuff. The distinction between life and non-life is an imperceptible continuum – lending further plausibility that the former can evolve slowly from the latter.

    #6 – not sure why you are confused. This is just saying, if life were created, it was created through a process that looks an aweful lot like evolution over billions of years.

  19. RickKon 28 Apr 2014 at 2:34 pm

    Awww, heck – Steve beat me to it. But since I typed it up offline, I’ll respond anyway.


    Point 1: I will happily address this point, but I want to understand your distinction between design and descent. Please give me a definitive example of an organism that was designed into existence and wasn’t the product of descent.

    The article you cite does not in any way refute common descent, it just discusses better techniques for building and tuning the “tree of life”.

    Point 2: This is not “begging the question”. If all current life genetically traces back to a common ancestor, that ancestor itself descended from even earlier life. What is your difficulty with this?

    Point 3: http://www.newscientist.com/article/dn16382-artificial-molecule-evolves-in-the-lab.html

    Point 4: Pasteur? In 2014 you are basing your opinion of origin of life (OOL) on the work of Pasteur? There is no begging the question – the organic molecules necessary for life exist in surprising variety in our solar system. What is your difficulty with this?

    Point 5: My statement was: “The exact point between non-life and life was likely as fuzzy and indistinct as the dividing line between Latin speakers and the first French speaker.” What is your difficulty with that? We have disagreements today over what is “alive” and what isn’t, just as we have debates over what is a planet and what isn’t. Why would the evolution of the first life be any different?

    Point 6: Which words didn’t you understand?

    You link to an article about Lynn Margulis. Why? Nothing she says conflicts with anything I’ve said, nor does it conflict with common descent or OOL research.

    How would you summarize our understanding of the origins of life, besides “we don’t know as much as we think we do”? We know more today than we did 200 years ago. How would you, Sonic, summarize that advancement in knowledge? What do YOU think we can state with high confidence about the origins of life?

  20. RickKon 28 Apr 2014 at 2:39 pm

    I misspoke – both Steve’s beat me to it. Thanks to both! 🙂

  21. BillyJoe7on 29 Apr 2014 at 6:59 am

    Lynn Margulis:

    From sonic’s link: “http://discovermagazine.com/2011/apr/16-interview-lynn-margulis-not-controversial-right”

    “Natural selection eliminates and maybe maintains, but it doesn’t create”

    “All visible organisms are products of symbiogenesis, without exception”

    “Our claim is that there’s no evidence that HIV is an infectious virus, or even an entity at all. There’s no scientific paper that proves the HIV virus causes AIDS”

    “I do think consciousness is a property of all living cells”

    “Bacteria are conscious”

I don’t consider my ideas controversial. I consider them right”

    After discovering that mitochondria and chloroplasts originated as bacteria, Lynn Margulis saw symbiogenesis everywhere and gradually moved into the fringe.

  22. Bill Openthalton 29 Apr 2014 at 7:46 am

    Margulis is not that controversial when she says that interaction between organisms contributes to (and might even be the main factor in) mutations. We know that genes can migrate from one organism to another, and mutations caused by interaction between organisms are no less random than those caused by high energy radiation — and probably a lot less damaging to the cells. From there to conclude that it’s only symbiogenesis is really quite a stretch.

    That being said, it is still natural selection that determines the gene combinations that make it into the next generation.

    Where Margulis really goes off the deep end is when she talks about HIV (where she is just wrong) and consciousness.

    The way she defines consciousness a thermostat is conscious. This is no problem per se, but she strongly hints at a conscious purpose driving changes to organisms in a particular direction, and for this there is no evidence at all. It also promotes consciousness to a kind of substance, not merely a property of complex living systems (which it most likely is). It’s sloppy thinking – attractive maybe, but sloppy.

  23. sonicon 29 Apr 2014 at 11:42 am

    I didn’t say ‘common descent is wrong’, I just said it has been ‘over hyped’–
    that is to say I think there is a level of certainty displayed that goes well beyond the evidence… Not that the evidence is bad or the interpretations wrong– but I do find a good bit of room for doubt based on the evidence.
    I don’t have an alternative hypothesis.

    Allow me to explain my reasons for saying ‘over hyped’ and where the doubts come from–

    The article I linked to suggests difficulties in coming up with a ‘tree of life’.
    Yet, it is often promoted that such a tree exists, there is a match between numerous methods of construction, and this is proof of common descent.
    But there isn’t a tree and there are difficulties in trying to produce one from the actual physical evidence.

    That makes it over hyped. OK?

    (Reflexively contrarian? I’d agree, but that would make me a liar– but if I disagree that makes me a liar. Are you sure you aren’t a lawyer?)

    Dr. N.-
    I thought the molecular evidence was overwhelming until I found out about a few phenomena.

    There are three ways beside common descent that can explain sequence congruity-
    Horizontal gene transfer, viral insertions of introns, and convergent evolution.
    Any claim that a particular sequence could only come about by common descent is an overstatement.

    Another situation is the discovery of the extent to which what has been called ‘junk DNA’ isn’t junk, but has important regulatory functions.
    This brings into question the common premise that any non-coding congruencies that match are from common descent because-
    1) Other means have been observed to produce such sequences, and
    2) Regulatory functions could be under selection pressure and therefore be the result of convergent evolution.

    I was told there is a tree (there isn’t), that ‘common descent’ is the only explanation for certain congruences (it isn’t) and that there is lots of ‘junk DNA’ (more questionable by the day).
    My certainty level has not increased as time has gone by.

    Should it have? I have no alternative hypothesis.

    It is possible that one day we might be able to define life- or we might not.
    I’m not sure that’s because that’s how life is or that we are ignorant.
    I remain suspicious that we are ignorant. I know I am.

    Sorry for the use of the term ‘design’. I have no means of detecting design, so while I can imagine the possibility, I don’t think it is a particularly scientific notion.
    I’ll leave off that.

    The evidence that ‘life comes from life’ is experimental.
    This is a paradox as it doesn’t have a logical way to start–
    You assume it started a certain way– not a way that has ever been demonstrated, but a way that you assume must be the way it happened.
    That’s called ‘begging the question’.

    That’s a good article in ‘new scientist’, but I’m not sure it is meaningful– from that article–
    “More fundamentally, to mimic biology, a molecule must gain new functions on the fly, without laboratory tinkering. Joyce says he has no idea how to clear this hurdle with his team’s RNA molecule. “It doesn’t have open-ended capacity for Darwinian evolution.””

    Check here as well-

    I’m not sure how convincing those results are to someone who doesn’t want to be convinced.

    Yes, Pasteur took all the ‘organic molecules necessary for life’ and put them together. And no life has come from it yet.
    So given all the ‘building blocks’ we still don’t get life. The fact that a ‘building block’ has been found on an asteroid or whatever isn’t really a big deal.

    My problem is this- is our current inability to define life something that will be forever?
    If not, then we argue from ignorance when we draw conclusions due to our current inability to define the term clearly.
    Of course it might be that we can’t find a line because there isn’t one. That’s doubt.

    I would say that we can say with high confidence the actual experimental results-
    All known life comes from previously existing life.

    At this point it seems clear that one assumes there is a chemical origin because one wants to generate testable hypothesis.
    But I’m not sure ‘life came from inanimate matter’ is a falsifiable hypothesis.
    Oddly, the notion that life can’t come about that way is falsifiable, but currently it seems this doesn’t lead to testable hypothesis.

    I think this is a concrete example that scientists prefer testable hypothesis over falsifiable ones when that is the choice. (Often hypothesis can be both).
    How about that?

  24. steve12on 29 Apr 2014 at 2:24 pm


    I want someone to explain this to me:

    Given 3 elements that no one debates the existence of: genetic heritability + feedback from the environment on who passes those genes on and who doesn’t + a shitload of iterations, how does a tree NOT form?

    Is there some magical biological force that says “Oh no!!! You are MUCH too different than your ancestors! No more changin’ for you kiddo!”

    It’s so simple, really. Given the mountains of convergent evidence, no competitors, and mechanistic destiny, common descent is as assured as gravity. The only debating left is based on politics or attention seeking behaviors (ahem).

  25. Steven Novellaon 29 Apr 2014 at 2:42 pm


    I disagree with your interpretation of the state of the science. You appear to be making a serious category mistake which is not uncommon – you are assuming that deepening knowledge as to the complexity of a system undermines our confidence in the more basic facts of the system. This is not true.

    Specifically – there absolutely is a tree of life, in that there is a dominant pattern of nestled hierarchies of living creatures. There are monkeys within primates within mammals within vertebrates, etc. Horizontal transfer of genetic information is a detail, a relatively small footnote on the overall tree-pattern. It does not in any way call into question or reduce our confidence in the basic truth of the tree.

    You are also mistaken on the molecular evidence, which overwhelmingly supports common descent. There are mutations that are invisible to selective pressures, such as silent mutations that do not affect amino acid sequence. These can be shown to drift at a fairly steady rate, free from selective pressure. What we see, for any protein examined, is that the degree of this molecular drift of silent mutations fits into the overall pattern of the tree of life.

    The amino acid sequence of hemoglobin between humans and chimps is identical, but not the base-pair sequence. Why not? If they were created at some point in the past you might argue that they started out as identical, then drifted apart from there. However, when we look at other animals we don’t find the same degree of drift that we would predict from a single creation. We find different degrees of drift proportional to evolutionary distance. The farther back in time the common ancestor, the greater the genetic drift. This is true without exception for every protein examined. This is only compatible with common descent.

    Viral insertions show the same pattern. Creatures with common ancestors share viral insertions possessed by the common ancestors, but not acquired after the split. We can say this because we can look at many species and see the pattern – the same tree of life pattern that all other lines of evidence converge on.

    I also disagree on junk DNA. Most of what was believed to be junk is still junk. There has been some nibbling around the edges, and a little bit now seems to have regulatory functions (or at least effects, it remains to be seen if they are necessary) but estimates are not just based on whether or not we know the function, but also looking at which parts of the DNA appear to be mutating under no selective pressure. We now also have the additional line of evidence of engineering bacteria and yeast with simplified genomes with “junk” removed, and they seem to do just fine.

    Science generally digs deeper with time. We find increased complexity and exceptions, but this does not change the basic facts. That DNA is the molecule of inheritance is not brought into question because of the discovery of epigenetics, it’s just another layer of complexity.

  26. RickKon 29 Apr 2014 at 4:12 pm

    Darnit – I typed this up offline and have been scooped by the Steves again.


    I’m less familiar than others are with your stance on these issues. Are you indeed a creationist? Are you arguing from a default position that an “intelligent supernatural agent” is a reasonable starting proposition? Your questions sound very much like you are.

    “Common Descent” does not mean “From one individual, with every generation fully mapped out and understood, with no gene transfers or symbiosis of any kind along the way”. It means that the current diversity of life grew out of a common, limited gene pool (like, you know, a “species”). Yes, there were lateral gene transfers – so what? In fact, that common ancestral gene pool may very well have been swapping DNA like kids swap baseball cards – so what? Yes, there were DNA insertions – so what?

    If you get a retrovirus infection in your gonads and pass a viral DNA insertion to your offspring, does that break the descent lineage from your grandparents to your grandchildren? No.

    You’re sounding very much like a creationist who points to a gap in the fossil record and claims it is evidence against evolution.

    It is not begging the question to say that the common ancestral species or gene pool was itself the result of evolutionary processes (my words). ALL life we’ve studied in nature is the result of evolutionary processes. My statement is as controversial as saying all furniture is made of atoms.

    As for the tree of life – again, you sound like a creationist (or a bad sensationalist journalist) claiming some DNA-swapping invalidates the nested hierarchy model of the evolutionary tree. It doesn’t.

    You also seem to have a real problem with the fact that the line between non-life and life was likely very fuzzy. I’ll use my earlier analogy: the fact that we can’t name the first French speaker doesn’t mean that French didn’t evolve from Latin.

    You wish to conclude that we’ve learned nothing in 200 years about the origin of life. But that’s not accurate – we’ve come MUCH closer to understanding the critical transition point. There are still many discoveries ahead, and we may never recreate the exact mechanism that started the first life. None of my statements claimed otherwise.

    But we know something even more fundamental (than life comes from life) from millennia of testing: natural events have natural causes. Origin of life research is not about proving life DID evolve naturally from non-life, it is about determining HOW life evolved naturally from non-life.

    Self-replicating, evolving molecules, genetic studies, early Earth research, molecular biology – these are all filling in the puzzle pieces and adding to our knowledge of how life evolved from natural causes. ALL the evidence continues to point to natural origins and natural processes. If you don’t want to be convinced, that’s your choice, but don’t kid yourself that your doubt is reasonable or has a basis in evidence or logic.

  27. BillyJoe7on 29 Apr 2014 at 6:02 pm


    However much he may sound like a creationist and believer in supernatural agents and however often he quotes creationists and believers in supernatural agents (and fringe dwellers), sonic himself is neither. He does seem to be in favour of the idea that organisms can determine their own evolutionary future, though he is a bit wishy washy about what he means by “determined”.
    I think you have him in a nutshell with the following…

    “If you don’t want to be convinced, that’s your choice, but don’t kid yourself that your doubt is reasonable or has a basis in evidence or logic.”

    He does have unreasonable doubt, inherited from reading too uncritically, the blatherings of science fringe dwellers. I don’t think he would disagree with too much of what Steven Novella has written above, just the degree of certainty with which he says it. If only he would approach the fringe dwellers with the same degree of doubt he would be halfway to somewhere.

  28. RickKon 29 Apr 2014 at 6:52 pm

    Thanks BillyJoe7,

    The origin of life is one of the greatest stories in the universe – there’s no denying the objective truth of that statement. While we certainly don’t want to claim more knowledge than we have, we also don’t want to deny the knowledge we have acquired through hard, persistent, rational enterprise.

    Enough of the mysteries of nature that we’ve answered have had natural causes (all of them, actually) that we can state with high confidence (the term I used before) that life had natural causes. We can state with high confidence that there was a time before life on Earth, so we can state with high confidence that natural processes took us from non-life to life. And with more recent findings, we can state with high confidence that evolutionary processes were involved in the formation and development of the first life, regardless of how fuzzy that starting point may have been.

    Sonic clearly wants another answer. My fear is that he will view the value of new evidence not for what it tells us about the high-confidence narrative, but for its value in diverting the narrative to the answer he seeks. That’s unfortunate, because just like creationists, he may have little or no appreciation for the awesome wonder that the rest of us feel as these new discoveries are made and the puzzle filled in.

  29. RickKon 29 Apr 2014 at 7:29 pm

    Ah, I found the essay I was looking for – the original source for my list.

    Another view on what we actually know about origin of life research – and that was 6 years ago.


  30. tmac57on 29 Apr 2014 at 8:38 pm

    sonic-“My problem is this- is our current inability to define life something that will be forever?
    If not, then we argue from ignorance when we draw conclusions due to our current inability to define the term clearly.
    Of course it might be that we can’t find a line because there isn’t one. That’s doubt.”

    Well,since ‘life’ is a concept that humans came up with,then whatever it is is whatever we define it to be. It’s not that there is necessarily ignorance about life, but that it is a fluid concept due to the changing understanding of biological processes,and experimental observation. It isn’t as though there is some ‘life’ property of the universe that we are trying to unravel,but simply a label that we assign to a category that we call life,much like the way we categorize many things ,there exists a continuum of known objects,from quarks to the universe as a whole,but we are the ones naming and defining those things,not the things telling us what they are.
    Finding out where we logically want to assign the name or concept of a certain thing in our world is not a process of “arguing from ignorance”,it is a process of overcoming ignorance.

  31. BillyJoe7on 30 Apr 2014 at 7:16 am

    sonic: ”My problem is this- is our current inability to define life something that will be forever?”

    Yes, and it matters not one iota.

    The probability that we will ever be able to define life so as to clearly distinguish it from non-life is about as likely as being able to define adulthood so as to clearly distinguish it from adolescence.
    But, how is that a problem?
    We can speak about life and non-life without being able to clearly define the difference between them, just as we can speak about adults and adolescents without being able to clearly define the difference between them.
    Moreover, and more to the point, the fact that there is no clear dividing line between them means that, at the interface between non-life and life, there is not much difference between non-life and life and, therefore, not much of a hurdle to jump in getting from non-life to life.

    In other words you are making Rick’s argument for him.

  32. The Other John Mcon 30 Apr 2014 at 9:03 am

    “you are making Rick’s argument for him”…Good point BJ

  33. sonicon 30 Apr 2014 at 9:38 am

    Dr. N.-
    Let’s break this problem into pieces- I’ll give a specific example of something that has lowered my confidence in common descent —


    “Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes,” Lynch said. “This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.”

    In the past, the explanation for these sequences was common ancestry/descent.
    But now there is another explanation.
    My confidence in the first explanation is reduced due to there being another possible explanation.

    Clear enough?

  34. SteveAon 30 Apr 2014 at 10:58 am

    Sonic: “Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes,” Lynch said. “This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.”

    How is this an argument against common descent? It’s a detail. If ten thousand people cross a river on a ferry and one person swims, the one swimmer does not negate the existence of boats.

    Also note that the ‘indepedent genotypes’ are of different lineages of the same Daphnia species. Why would the ‘hot spots’ that allow the introduction of introns themselves not be a product of common descent?

  35. RickKon 30 Apr 2014 at 3:21 pm


    You are raising the same arguments in the same way as the Discovery Institute. This very paper was argued this way on evolutionnews.com. If you’re not a creationist, you’re going to a lot of effort to sound like one.

    You sound like an anomaly hunter – blowing tiny exceptions out of proportion in an attempt to push the mountain of evidence closer to the narrative you desire. It is the height of motivated reasoning.

    A bit of soft tissue found in one fossil does not raise serious questions about the age of the Earth.

    An odd shadow on a photograph doesn’t raise serious questions about the reality of the Apollo Moon Landings.

    A segment of DNA that shows higher rates of variability than expected does not raise serious questions about common descent.

    Unless, of course, you are willing to sacrifice rationality and perspective in pursuit of your own fringe narrative. Then any anomaly will do.

  36. grabulaon 30 Apr 2014 at 9:56 pm

    Sonic strikes me as having a creationist background. His arguments sound strikingly similar to the arguments my boss makes and ultimately come from creation.com. I noticed, and pointed this out in my own discussion that creation.com often tends to attack minor discrepancies as if they were glaring evidence for something. They have hundreds of articles attempting to use science against itself. Science says this may have happened so it has to be wrong about this other theory. They grasp at the fringe in the hopes of sounding legitimate to the layman. I can tell my boss is having that issue, the science is beyond his current understanding and so he falls easily into an argument that supports his beliefs without really understanding the underlying issues.

    He even fell on the ole Ken Ham argument that if we can’t or don’t see it happening at this very moment, how can we know for sure it happened the way we think it did?

    Please tell me sonic that at the very least that kind of reasoning is irrational to you?

  37. AmateurSkepticon 01 May 2014 at 7:18 am

    I would love to know what is the state of the science regarding the creation of life. What steps are believed to be still unknown?

    Of course, opinions regarding future events will vary but are we likely decades away or centuries away from the laboratory creation of life.

  38. BillyJoe7on 01 May 2014 at 7:50 am

    sonic: “I’ll give a specific example of something that has lowered my confidence in common descent:

    Sonoc quotes Lynch as saying:

    “Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes…This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor”

    Lynch also said the following:

    “The immediate question will be whether our findings can readily be extended to other species”

    “In addition, there is need for some solid molecular work to test our hypothesis about the mechanism of intron origin”

    “Our molecular analyses have enabled us to reject a number of hypotheses for the mechanism of intron origins, while clearly indicating an entirely unexpected pathway — emergence as accidents arising during the repair of double-strand breaks”

    So here we have a single paper – which has not yet been replicated as far as I can tell – about a single species of water flea, which has not yet been shown to extend to any other species, and for which the mechanism has not been elucidated except for a clear indication that it involves accidents (= random mutations) during repair of double strand DNA breaks (the repair mechanism itself being the result of random mutation and non-random selection).

    And this somehow lowers sonic’s confidence in common descent!

  39. sonicon 01 May 2014 at 9:25 am

    Thank you very much for commenting on the article I linked to.
    You are correct– that result lowers my confidence… and you are right, it is hard to know by how much because I’m not certain how ubiquitous the phenomena is.
    Very good point.
    So the confidence is lowed by some amount– maybe very small, maybe quite a bit– it isn’t clear yet.
    Thank-you very much– that is what I’m saying.

    Now, can we discuss the lowered confidence due to the findings regarding ‘junk DNA’?

    You aren’t sure if there is a difference between life and non-life.
    But just a little while ago you were assuring me that it isn’t OK to kill someone.
    There’s a pretzel in that logic that has my circuits in a gordian knot. 🙂

    The argument for common descent consists in part from the DNA sequences.
    Those sequences that are ‘non-coding’ yet very similar have been considered proof of common ancestry/descent.
    Now we have another explanation for the phenomena.
    If you had only one possible explanation, and now there are two possible explanations, then the confidence that it has to be the one is reduced.

    Is there something wrong with that logic? Can you specify the error please?

    You say ” origin of life research is not about proving life DID evolve naturally from non-life, it is about determining HOW life evolved naturally from non-life.”

    If I were a scientist, I would assume that premise as a research hypothesis.
    As a non-scientist, I don’t feel the need to know how life began without demonstration. So, as the hypothesis is yet to be demonstrated, I feel no compunction to have a certainty as to the outcome of future research.

    Your retreat to name calling is sad.

    I really don’t know what future discoveries will be made regarding the origins of life or how life is best defined.
    I fear this ignorance on my part precludes any meaningful discussion on this topic with you because my questions are in large part due to my not knowing those futures.

    Do you understand the logic- if you have only one explanation for a phenomena, then when you see the phenomena, you have great confidence in the explanation.
    But suddenly there are more than one possible explanation for the phenomena. This causes a reduction in the certainty in that the one explanation is correct.

    Does that seem rational to you?

  40. RickKon 01 May 2014 at 12:39 pm


    I KNEW you would do that. I knew you would ignore my list of items that we know with high confidence. I knew you would focus on that one line. And I knew you would equate my term “high confidence” with “certainty”.

    So, in the interest of accuracy and honesty, let’s review. In which of these statements do you lack high confidence?

    – Natural phenomena have natural causes
    – Life is a natural phenomenon
    – There was a time when there was no life
    – There is now life
    – Therefore origin of life research is the search for the natural causes that brought life from non-life

    I assume your opinion on these matters is based on evidence and logic. So if you lack high confidence in any of the above statements, please present the evidence.

  41. Steven Novellaon 01 May 2014 at 1:08 pm

    Sonic – you ignored my offer of several lines of evidence supporting common descent. The other commenters did a great job of exposing your poor logic and motivated reasoning in this case – anomaly hunting and then jumping to unjustified conclusions.

    The paper you cite does not call into question common descent. As pointed out, it shows only intron hot spots in varieties of one species. It’s important for how to interpret the history of descent within one lineage – not the reality of common descent.

  42. steve12on 01 May 2014 at 1:29 pm

    You guys have a LOT more patience than me!

    But that’s good. I think when these types of arguments go unchallenged, some might thin they have some sort of validity.

  43. sonicon 01 May 2014 at 3:19 pm

    Guys, I would be happy to discuss the evidences for.
    In fact, I was discussing what I thought was an excellent evidence for, the DNA sequences.
    I gave an example of why the evidence isn’t as airtight as it seemed at first (an explanation for sequence congruity other than common ancestry/descent).
    You come back with -‘what about the others?’– certainly a good question and one I be happy to take up, but what is the point if you can’t accept that the phenomena from the study I linked to might have an impact on the certainty one would have about the analysis of the DNA sequencing?

    I haven’t even made a controversial claim and I have been called names and the actual argument ignored.

    Actually BillyJoe7 got it right– the result does bring questions, but we really don’t know enough about the phenomena to be certain to what extent it is important.
    He pooh-poohed the difficulties, but at least he saw what I’m talking about.

    How can we go forward if I can’t draw a logical conclusion from an experimental result without being attacked with name calling and then have the conclusion ignored as if it doesn’t matter?

  44. RickKon 01 May 2014 at 3:43 pm


    Questioning common descent based on a finding about intron insertions in a species of daphnia is not a logical conclusion. In fact, you’ve yet to raise a single piece of evidence that brings into question the common descent of life on Earth.

    Of my original list to grabula, you’ve not raised a single argument that justifies your doubt in any of them. In most cases, as Steve and I both pointed out, you missed the point entirely. Whether this was a lack of comprehension, or an intentional ploy so you could argue against strawmen of your own creation, I don’t know.

    When I attempt to rephrase questions more clearly, you ignore the attempt and circle back to your anomaly, a finding that didn’t in any way question common descent or the tree of life. All it did was offer a tiny addition to our knowledge of how to arrange twigs on the end of one of the tree’s branches.

    Finally, calling you an anomaly hunter who uses the same arguments as creationists is no more controversial than calling you an English speaker. Retreating into indignation over an imagined slight is one way for you to duck and run, but it doesn’t help your cause or bolster the respectability of your position in this discussion.

  45. Steven Novellaon 01 May 2014 at 4:50 pm

    Sonic – we did answer your evidence. As Rick just reiterated – at best it informs how we would assemble a cladogram when we get to the end of a twig on the tree. It is not as if congruity of intron locations within a genus is a major pillar in the evidence for common descent.

    It is exactly like saying that because we have discovered epigenetic factors influencing phenotypes, that this calls into question whether or not DNA is the molecule of inheritance. No – it doesn’t.

  46. RickKon 01 May 2014 at 6:48 pm


    Sorry – missed your post. I hope you’re still checking in.

    Two sources for Origin of Life material are:



    And Wikipedia, of course.

    Yes, I would guess we’re a long way off from creating life from scratch in a lab. Maybe we’ll look at the problem in a different way and have a breakthrough. Maybe we’ll discover early proto-life elsewhere in our solar system and that will give us some critical insights. Who knows?

    As with many facets of our universe – we’ve learned a lot, but there’s much more to learn.

    It is possible that the pathway from non-life to life is difficult and improbable, so infrequent that it only happens occasionally in a universe of ~ 10^23 star systems over billions of years. If so, we may be working on the puzzle for a long time.

    But we can say with high confidence that the process does happen – because we’re here now and we weren’t always. 🙂

  47. grabulaon 01 May 2014 at 9:24 pm


    We still don’t’ really know how life began – abiogenesis. There are some promising theories bu there is still a lot of work to do on it before we really having something robust to speak about. That however is why creationists and the like are focusing more and more on attacking the concept. They mistake the lack of knowledge for a weaknesses in the scientific method, or a strength in their argument for creationism when it isn’t. As someone pointed out, it’s similar to the problems of round vs flat earth, geocentricity and a whole plethora of scientific discoveries that just took time to come to fruition.


    What frustrates me most about people who come to this blog and claim to be looking for honest discourse opposing consensus views is that they almost inevitably reveal they are not interested in honest discourse. Take this discussion for example. Several of us have replied directly to you explaining the errors you’ve made, most of which are fairly obvious once you read the links you’ve provided. But as seems to be almost always the case instead of graciously accepting the honest opinions and rebuttals to your claims, you continue to ignore us. You claim we’re ignoring your arguments – which we haven’t, though you’ve most definitely ignored ours. You claim we’ve name called and attacked you – I’m not seeing, though admittedly there comes a point where we realize you’re being extremely obtuse or purposefully disingenuous and then it becomes more and more difficult to take you seriously.

    My advice to you would be to first go back and read the article you linked and try to think for yourself on why it definitively does not support your claims. If that doesn’t help, examine the thorough explanations you’ve been provided on this discussion to go back and examine what the article is actually saying.

    You absolutely cannot have honest discourse if you continue to insist on being dishonest, and you will not be taken seriously if you continue to follow the pattern you’ve chosen to take.

  48. AmateurSkepticon 02 May 2014 at 4:09 am

    Thank you very much RickK.

    I had been hoping that you would say “Well, as a matter of fact, I’m working on that….. any minute now”. However, as in “life” so often the real answers just aren’t the one which you had been hoping for.

  49. BillyJoe7on 02 May 2014 at 7:49 am


    “You aren’t sure if there is a difference between life and non-life”

    What a mischaracterisation of what I said!
    Here it is again:
    “Moreover, and more to the point, the fact that there is no clear dividing line between them means that, at the interface between non-life and life, there is not much difference between non-life and life and, therefore, not much of a hurdle to jump in getting from non-life to life”
    A little phrase you conveniently glossed over: “at the interface”.
    Is a virus alive? Some say yes, and some say no, and there are good arguments on both sides. In other words, we can’t really tell for sure whether viruses are a form of life or a form of non-life. So “at the interface” there cannot be much difference between life and non-life.
    Which makes your following comment totally and completely irrelevant…

    “But just a little while ago you were assuring me that it isn’t OK to kill someone”

    You, on the other hand, seemed to think it was okay for parents to kill their children if that was in line with their religious beliefs because personal freedom is paramount and we can’t have governments telling people what they can and can’t do and, anyway, it would prove too costly to stop them doing so.
    Frankly, I’m surprised you aren’t too embarrassed to bring that discussion up again

  50. sonicon 02 May 2014 at 3:41 pm

    You actually addressed the point of the article I linked to– thank you.
    I look for reasons to doubt.
    You think I look too hard.
    I don’t dislike you for your incorrect opinion about this– after all, it’s possible that your ‘incorrect opinion’ might actually be right and I am looking too hard for reasons to doubt.
    But I doubt that.
    Are you understanding me any better?

  51. sonicon 02 May 2014 at 3:41 pm

    Dr. N.
    Thank you for your patience.

    I imagine this reply–

    “The article linked to gives an apparent example of a phenomena that would decrease confidence in common descent as the explanation for similarities between DNA sequences.
    At this time we don’t know if this phenomena occurs often, or maybe this team made an error, or any number of other possible situations, so it needs to be further investigated before we can determine how much this phenomena matters, if at all.

    As this example is questionable and there are other lines of evidence that favor the interpretation of common descent, this example of a possible phenomena isn’t enough to materially impact my thinking regarding the certainty of common descent.

    Is that all you’ve got?”

    Or something like that.

    I would say- ‘Yes, I’m looking for reasons to doubt– perhaps I’m looking to hard in this case– but I’m taking it as a reason to doubt– I understand why someone would not.”

    Or something like that.

    I could then bring up the next point- it could be discussed in a like manner and we could come to some understanding as to why we take the positions we do.

    Oh well, my imagination has been called ‘wild’ before, perhaps this is just another example of that.

  52. sonicon 02 May 2014 at 3:41 pm

    I have read what you wrote back to me- but you haven’t addressed the phenomena I’ve linked to in a meaningful way.
    The simplicity is this– an observation was made that two genomes can look like they came about through common ancestry (descent) without them actually having done so.
    Can you see how that would reduce confidence in the idea that sequences being the same is evidence for common ancestry/descent?

    If so, just say so– then you can tell me why it isn’t a big deal.
    If you don’t understand why such an observation would reduce certainty, then I have to explain the phenomena in such a way that you might so that we can discuss this rationally.



  53. RickKon 02 May 2014 at 7:02 pm


    Let’s be very clear – you didn’t start this discussion by saying that intron insertions lower your confidence in common descent by 1%. You started by fundamentally doubting the whole concept of common descent, and declaring the branching tree model of species evolution is invalid.

    Now you appear to be retreating to a position of saying “well, isn’t it logical that this intron paper would reduce my confidence in common descent by just a little?” You’ve avoided or retreated from every other argument in this discussion, so this is not surprising.

    But to address your pet anomaly more thoroughly:

    The intron evidence is consistent with a small subprocess about which we have more to learn. It is not consistent with a fundamental failure of common descent. Why do I have high confidence in this conclusion?

    Because an intron is not a genome just as a twig is not a tree.
    Because the authors of the paper did not question common descent because THEY knew their findings didn’t call it into question.
    Because many incredibly rich lines of evidence support common descent – lines which Steve has offered twice to explore with you but you doggedly stick to your anomaly.
    Because thousands of biologists have worked their entire careers building on the concept of common descent.
    Because we make predictions that come true, and could only come true if common descent were true.
    Because common descent is the only model that fits the evidence without introducing magic.
    Because falsifying common descent is an extraordinary claim, and the introns don’t qualify as extraordinary evidence.

    What you are doing is precisely comparable to someone pointing at a shadow in a photograph and claiming it raises real doubt that Apollo 11 landed on the Moon.

    Sonic, here is a valuable life lesson: when you do a little internet browsing and make a discovery that proves that thousands of experts who’ve dedicated their lives to the subject have made a major fundamental error, you are wrong. Period.

    You are not convinced because you are ideologically committed to your position, not because you’ve actually considered the issue and the weight of evidence. You said it yourself – you’re not honestly looking at the weight of evidence, you’re just looking for any little reason to justify your pre-established doubt. So, I will no longer try to reason you out of a position you didn’t use reason to attain. I consider intentional blindness a form of dishonesty, and I see no value in trying to reason with an intellectually dishonest person.

  54. BillyJoe7on 03 May 2014 at 1:25 am


    It is good to look at the detail, but not at the expense of the broader picture.

    Do you ever go to an art gallery?
    You look at the piece from a distance to get the overall view. But even the most artistic piece will have a flaw somewhere, maybe even several. But that doesn’t change your overall assessment of the artistic merit of the piece. The brush stroke that went a little too far, or the shadow that stopped a bit too short does not destroy the painting.

    Do you ever venture into the mountains?
    Your senses are heightened as you approach from the valley floor and you immerse yourself in the sights and sounds as you hike up the mountain trails and run down the other side. You come back satiated and refreshed, filled to brim with what you’ve just experienced. Did you see the scarred and fallen trees? Of course you did. Did it detract from the experience? Of course it did not.

    Common descent is as solid as rock and no small detail is ever going to crush it underfoot. The tree of life is real and no spider webs in the twigs is ever going to send it crashing to the ground. And no metaphorical socialising amongst nominally conscious bacteria is ever going to throw into the dustbin of history the major driving force of evolution.

  55. BillyJoe7on 03 May 2014 at 7:47 am

    Which reminds me…

    Tomorrow is May the 4th (Star Wars Day).
    I’ll be running in the 33rd annual Great Train Race.


    May the force be with you. 🙂

  56. RickKon 03 May 2014 at 12:30 pm

    I opened the refrigerator and there was a pomegranate.

    Now, the “preponderance of evidence” points to the conclusion that my wife put it there. After all, nobody has ever witnessed spontaneous generation of a pomegranate in a refrigerator. Every other case I’ve heard of where a pomegranate entered a refrigerator involved the direct actions by someone, usually the owner of the refrigerator. And my wife has been the cause of most of the other appearances of objects in our refrigerator.


    I’ve not blindly bought into materialist dogma of the “wife-pomegranate-refrigerator” narrative. A pomegranate? That’s highly unusual. I’ve never seen a pomegranate in our refrigerator before. I don’t recall even seeing pomegranates on sale around us before. I don’t share the confidence that my daughters display when they state with such certainty that “Mommy must have bought it and put it there!”. Such is the influence of their dry, secular public school education.

    But I have good reasons to doubt that mainstream just-so story.

    First, nobody has ever proved that the only way for an item to enter a refrigerator is by someone putting it there. I myself have heard people exclaim, when opening a fridge: “how did THAT get there?”. There are plenty of undiscovered forces in this universe – at least undiscovered by science.

    Second, there was a wavering glow in the night sky just visible through the trees in our back yard last night. There are no houses there, so the best explanation is an other-wordly force at work. And I don’t have enough faith to just brush off this visible energy phenomenon and the appearance of the pomegranate as mere coincidence. The world is so much more complex than people will allow themselves to admit.

    Finally – a pomegranate? This is the part that none of the close-minded people around me understand. If I were a visitor from another planet or plane, this is exactly the kind of tactic I would employ. By placing an object so heavily laden with spiritual meaning in an otherwise ordinary place, only a truly open-minded individual would appreciate the significance of such an event and would start asking questions. Such a person (me, in this instance) is EXACTLY the kind of person an alien race would want to engage in first contact. This must be how they identify those of us to approach.

    My wife now insists she bought the pomegranate as a novelty at the local grocer and put it in the refrigerator. But it is too late – I’ve already learned what I needed to learn. Besides, I could see the flicker in her eyes as she said it. I know she thinks she was just humoring me, trying to keep me off the scent of a truly life-changing revelation. She’s so bounded by her self-described rationality, and so incapable of thinking beyond her naturalistic little world, that I’m sure she even believes her own story now. She couldn’t live with the cognitive dissonance otherwise.

    But I’m the one with the open eyes and open mind, and I know better.

  57. sonicon 05 May 2014 at 9:23 am

    I did not ever say the ‘branching tree model of species evolution is invalid’.
    Perhaps you have been discussing things with a straw man you have erected in my place.

    I have ‘retreated’ to my opening position- one which you failed to acknowledge– perhaps because you were too busy arguing with someone who isn’t here.

    If you can’t acknowledge that given one explanation for a phenomena– then suddenly there might be two explanations — that would lower one’s confidence that the one is correct, then what is the point of trying to communicate?
    And you actually deny that– don’t you?

    So, you have lied about my position, you have refused to acknowledge a simple fact, and now you want to say I’m being dishonest.

    Perhaps in the future you could engage with my actual position on this matter.
    I notice from the ‘pomegranate’ story you are still engaged with a straw man.

    I hope you had a good race.

    I think it is valid to question things– when a new phenomena is observed– for example.
    You seem to think certain things are beyond question– it doesn’t matter what the evidence.
    It seems you are demanding I unquestioningly believe in things that have not been demonstrated and that questioning is wrong.

    But it’s so easy for me to find reasons to question–

  58. RickKon 05 May 2014 at 12:21 pm


    True to form, I see that your response does not in any way engage with the core of my response to your prior post. All those sentences starting with “Because…” were in response to your post, but you didn’t engage on the core argument.

    As for your strawman accusation: my view of your starting position is based on your statements that the concepts of common descent and a tree of life are “over-hyped” – meaning they could be fundamentally flawed. Your position is clearly stated here:

    Sonic: “The article I linked to suggests difficulties in coming up with a ‘tree of life’.
    Yet, it is often promoted that such a tree exists, there is a match between numerous methods of construction, and this is proof of common descent.
    But there isn’t a tree and there are difficulties in trying to produce one from the actual physical evidence.”

    To which Steve responded:

    “..you are assuming that deepening knowledge as to the complexity of a system undermines our confidence in the more basic facts of the system. This is not true.
    Specifically – there absolutely is a tree of life, in that there is a dominant pattern of nestled hierarchies of living creatures. There are monkeys within primates within mammals within vertebrates, etc. Horizontal transfer of genetic information is a detail, a relatively small footnote on the overall tree-pattern. It does not in any way call into question or reduce our confidence in the basic truth of the tree.:

    So I was not alone in interpreting your opening position as: “there isn’t a tree” because you said “there isn’t a tree”.

    Which part of “there isn’t a tree” did I misinterpret?

    What part of “It does not in any way call into question or reduce our confidence in the basic truth of the tree” did you not understand?

    You accuse fundamental principles like common descent and the tree of life as being “over-hyped” in spite of the numerous lines of evidence supporting them and in spite the numerous challenges they’ve endured from much more knowledgeable critics. You ignore or refuse to engage with evidence that contradicts your position. You flog (repeatedly return to) the intron study. You promote with confidence YOUR interpretation of the data, when even the study authors don’t say the data conflicts with common descent. And you give excessive weight to the importance of your interpretation in determining the validity of the tree of life and common descent.

    In short, you are actively and doggedly practicing the very definition of “over-hype”.

    Sonic, help me understand something. How is your over-hyping of your interpretation of intron insertions any different from Rhawn Joseph’s over-hyping his interpretation of the rock on Mars? How do you distinguish your mode of argument from his?

  59. BillyJoe7on 06 May 2014 at 6:51 am


    “I hope you had a good race”

    Thanks. yes I did. The weather was ideal – 7 degrees C, a drizzle of rain, and light breeze – for hill running. But I missed out to the train this year which beat me by 38 seconds. I blame my right achilles tendon which complained on the uphill sections. It was okay last Friday and again this morning, so I’m not sure what happened on Sunday. But the run was a great experience as usual.

    “I think it is valid to question things”

    No problem, except that if the weight of evidence is against you, you’ve got an uphill battle.
    For example, I’m not going to go into bat for flat earth.

    “You seem to think certain things are beyond question– it doesn’t matter what the evidence”

    Nope. Nothing is totally beyond question, but there are many things that are scientifically established fact. If the evdence all converges on one hypothesis, that hypothesis becomes a fact. Of course, even facts in science can be overturned given sufficient evidence. But that is simply not the case with your referenced paper.

    “It seems you are demanding I unquestioningly believe in things that have not been demonstrated and that questioning is wrong”

    Questioning is not wrong per se. But you lack perspective on many scientific questions. You cannot knock over well established scientific fact with a feather. Especially when those feathers are brandished by fringe dwellers and naysayers with axes to grind. And sometimes….

    “But it’s so easy for me to find reasons to question–

    …you just simply don’t understand what you read.
    That article offers absolutely no support for your claim that “there isn’t a tree”. That article says nothing about whether or not there is a tree. It claims that “the tree” is not usefull when considering which morphological features to preserve. It actually assumes there is a tree.

  60. sonicon 06 May 2014 at 11:48 am

    Here’s the problem– There is no tree of life from the physical evidence.
    That is a fact.
    It is now called the ‘web of life’.
    Here is a video you might like–

    So, there is no tree, but look at how it is demanded I believe there is.
    Over hyped.
    You might note– there are lots of ways webs come about.
    Is there a problem with what i just said?

    If I look at the ‘evidence for’ only I will draw wrong conclusions– for example– if I looked only at ‘successes’, then homeopathy works great– right?

    So, while I’m well aware of the evidence for– I’m also aware that isn’t the whole story. This allows me to see how the ‘evidence for’ drumbeat is hiding problems and is a form of ‘over-hyped’.

    The intron study points to a possible way that DNA congruities could come about other than common descent. I have acknowledged that the study is inconclusive as there is no way currently to know how ubiquitous the phenomena is. (Does Rhawn do that about the rock on mars?)

    You have refused to acknowledge that having more than one way something could happen would reduce confidence in the ‘one way’ only conclusion.

    It seems you are demanding agreement with things that are questionable and refusing to acknowledge possible problems with your position.
    I think that’s called being an ideologue– correct me if I’m wrong on that.

    It is difficult to ignore a complaining achilles. Even for achilles himself as I recall the story.
    If I could find an argument to go to bat with, I’d be willing to try the ‘flat earth’ thing. But I haven’t seen anything that made any sense at all on that. And you thought I had no standards… 🙂

    I agree– if all the evidence points to one thing… but what if all the evidence doesn’t? Do we ignore the bits that don’t?

    I agree- the intron paper doesn’t overthrow anything– it is an example of something that might.
    I have found it interesting that this can’t be acknowledged.

    I agree- the other paper assumes there is a tree and then points out that the evidence doesn’t confirm a prediction based on that understanding.
    That’s not falsification of the model, but it is not confirmation. In fact, it is an example of a difficulty with the tree model.
    But I thought there weren’t any.

    Over hyped.

  61. Bill Openthalton 06 May 2014 at 11:59 am

    sonic —

    You overplay your hand.

  62. Steven Novellaon 06 May 2014 at 12:12 pm

    Sonic – you keep missing or misrepresenting our position. It seems to me that you truly do not understand it. I will try again.

    The things you are pointing to do not call into question the underlying concept that life exists in a pattern of nestled hierarchies (some people use a tree metaphor to refer to this, but really we are talking about nestled hierarchies). This pattern is what would result from a branching history of relatedness, which is consistent with the view of common descent through evolution and speciation.

    It turns out, however, that parent to offspring (vertical) is not the only direction in which genetic information can flow. There are some mechanisms of horizontal flow, such as viral inclusions.

    The amount of horizontal gene flow, however, is dwarfed by vertical gene flow. It is interesting, but it is a tiny overall effect. It does not turn the tree into a web, but adds a few webs to the tree.

    Of course, popular treatments of science news items like to emphasize what is new and revolutionary, so they often exaggerate the overall impact of horizontal flow as if it “changes everything,” when it fact it is just an added layer of detail, but does NOT alter the overall pattern.

    The evidence for an overall pattern of nestled hierarchies within life on earth is overwhelming, and exists on the morphological, developmental, and genetic levels, and is further supported by fossil evidence showing a compelling temporal pattern as well.

  63. RickKon 06 May 2014 at 7:33 pm


    Thank you for such an apt example.

    Yes, if you cherrypick evidence (like looking only at successes), you may come to the conclusion that homeopathy works. And you would be wrong.

    Similarly, you cherrypick evidence (like your introns) you conclude that common descent and the tree of life (nested hierarchies) of species don’t exist. And you’re wrong.

    My consistent message is: don’t do that.

    What “one-way” are you talking about? The nested hierarchies of the tree of life are the natural outcome of the evolutionary model of descent with modification guided by selection – “evolution”. You’re accusing us of not acknowledging that your evidence supports another way. Another way of what? Intron insertions don’t change the parent/child relationships. They don’t change descent! All they do is offer another source of modification, like mutate pions, retro viral insertions, symbiosis, etc. So they in no way challenge the tree or common descent.

    Does a retrovirus insertion invalidate the relationship between you and your mother?

    Why can’t you just admit that they add details to the accepted model, they don’t overturn it?

    True to form Steve maintains his patience and tries once again to communicate with you and help you understand. Why have you refused over and over and over to engage with him on the full spectrum of evidence?

  64. BillyJoe7on 07 May 2014 at 6:17 am


    You could say my achilles was a kill-ease (credit to Douglas Hofstadter for that)

    But I’m surprised you can’t come up with flimsy evidence for a flat Earth.
    You seem to have no trouble with Evolution, GMOs, and Climate Change! 🙂

    What about that dam on your farm. The surface looks pretty flat don’t you think. Maybe that is evidence for a flat Earth. It might just blow the whole oblate spheroid theory out of the water.
    And the Sun definitely rises in the East and sets in the West. You can see that with your own eyes! Pretty good evidence against the heliocentric model don’t you think?

    So, I guess by those standards, the cobwebs destroy common descent, those socialising bacteria destroy modern evolutionary theory, WattsUpWithThat destroys climate change, and Monsanto destroys any argument for GMOs.

    Oh, I’m sorry, you merely think that it raises questions about the accepted science.
    It’s a pity you don’t question those naysayers, fringe dwellers, and shock jocks that you reference as doggedly as you question accepted science.

    “In fact, it is an example of a difficulty with the tree model”

    Nope. Read the article again. The problem was that convergent evolution made it difficult to judge which life forms – based on biological characteristics – should be conserved. Thats not evidence against the “tree model” at all. You have once again engaged in motivated reading.

  65. sonicon 07 May 2014 at 6:57 pm

    Let’s see if we can find a point of agreement here–

    A retrovirus insertion doesn’t invalidate the relationship between my mother and me.
    It might create a false signal of such a relationship however.

    From the article I linked to–

    “Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes…This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor”

    So the common assumption was there is only one way for the DNA sequences to share the similarity– it is always due to common ancestor. (This has to do with the assumption that mutations are random and that these sequence matches couldn’t have come about that way– so the sequence matches must be due to common ancestor/descsent.)

    But it turns out that there might be other pheneomena that explain the similarities.
    (HGT would be another example of this type of phenomena).

    It appears the signal for common ancestor/ common descent from the DNA evidence contains false positives, but it isn’t clear just how much this is a problem.
    Dr. N. asserts it isn’t much of a problem, but I can find examples of articles written by experts in this field that say the opposite. I think it’s debatable.

    Let’s find a point of agreement here–

    If the DNA sequences contain false signals of common ancestry, then any conclusion of common ancestry based on those sequences is less certain than they would be without the false signals.

    Would you agree with that?

  66. sonicon 08 May 2014 at 5:58 am

    I don’t mean to misrepresent your position.

    A lowering of confidence in a particular interpretation of one aspect of a complex subject is not equivalent to a repudiation of the entire subject.

    Sorry for any confusion on that.

    You seem to know what I think better than I do.
    I had no idea I thought any of those things! Amazing!

    I’m not sure– is it that the preacher will be righteous, or is it that the righteous will preach?
    I would consider your opinion on that matter definitive. 😉

    Trash talk aside– Let’s try again–

    From the article-
    “Some conservation strategies assume that the evolutionary distances between species on a phylogenetic ‘tree of life’ (a branching diagram of species popularized by Charles Darwin) can be used to predict how diverse their biological features will be.”

    Why would they assume that species further apart on the tree would have more different features and species closer on the tree would share more similar features?

  67. grabulaon 08 May 2014 at 6:35 am

    @ Sonic

    ” if I looked only at ‘successes’, then homeopathy works great– right?”

    No. Homeopathy doesn’t work so you would never see successes.

    “But it turns out that there might be other phenomena that explain the similarities.”

    And while that might contribute to the picture the overwhelming evidence points to other factors. This is like staring at a giagntic picture with your nose touching the canvas – all you can see is the red of the dress in the larger picture so your assumption is the entire picture must be red.

    BillJoe7 brings upa good point

    “It’s a pity you don’t question those naysayers, fringe dwellers, and shock jocks that you reference as doggedly as you question accepted science.”

    Do you spend as much time refuting actual sillyness or does your source of entertainment lie in flying in the face of stronger science?

    Some of you guys ‘just questioning’ get tiresome after a while. It’s the same pattern, you refuse to give ground in the face of evidence, you continue to cherry pick and anomaly hunt in the hopes of what? That possibly down the road you can say you were right?

    My interest in skepticism is looking for as much truth as I can get. While I love to see interesting alternative theories, and most of us do, I have no choice but to follow the evidence. That’s what kills me time and time again with you guys. You’ll squirm and twist to make something very tiny try to fit your alternate theories and then ask that you be taking seriously. What’s the point sonic?

  68. BillyJoe7on 08 May 2014 at 6:56 am


    “Why would they assume that species further apart on the tree would have more different features and species closer on the tree would share more similar features?”

    Because, amongst other factors, they failed to consider, or underestimated, convergent evolution.
    Don’t beleive me?
    Then listen to the author, Dr Robert Scotland:

    “Whilst ‘close neighbours’ on the branches of the tree of life are likely to share more biological features than distant ones, we found that you only have to move a short distance away before predictions about how much more diverse an organism’s features should be are no better than a random choice. Much of this may be down to parallel or convergent evolution that sees similar biological features – such as eyes and wings – evolving independently again and again throughout the history of life”

    This is the message of the article, not what your motivated reading massaged out of it.

  69. sonicon 08 May 2014 at 12:30 pm

    You didn’t answer the question-
    Why would they assume that species further apart on the tree would have more different features and species closer on the tree would share more similar features?

    Now the next question-
    What is the message I got from this article?

    If one views only the positive, homeopathy works every time someone who takes it gets better.
    And that happens quite often.
    You have presented no evidence in your comment, only vague claims about things that have nothing to do with the topic at hand.
    Are you a native English speaker?

  70. steve12on 08 May 2014 at 1:26 pm

    A LOT of patience!

  71. sonicon 08 May 2014 at 5:25 pm

    Dr. N.-
    I have gone off the rails a bit–

    A ‘tree of life’ implies a single trunk- a single beginning for all life (a miracle?)

    A ‘web’ allows for other possibilities– it could start in more than one place and grow together, for example. This implies a more ‘scientific’ kind of situation– something repeatable.
    Of course if life began de novo numerous times it opens all sorts of possibilities.

    That’s one reason the ‘web’ vs. the ‘tree’ matters in the discussion of the origins of life.

    I got side tracked about the levels of certainty people have when they discuss these matters.

    And appreciated.
    (Thanks for the poke).

  72. RickKon 08 May 2014 at 5:50 pm


    You’re making your same old category error – generalizing a debate about one aspect of genetics into a possible source of doubt about ancestry, and leveraging that conclusion into a bigger leap to rationalize your (pre-existing, ideologically-driven) doubt of common descent.

    So no, I do not agree that this new information casts valid doubt on common descent, because rearranging the twigs doesn’t invalidate the tree, and because introns are not part of the case FOR common descent.

    If you want to argue that parallel intron insertion casts doubt on common descent, first demonstrate some scientific consensus that introns are one of the pillars of evidence supporting common descent.

    But at the moment all you’re doing is arguing against a position that nobody is actually taking. Introns are not a component of the evidence for common descent. The ebb and flow of introns, the frequency, the source – these are all topics that have been debated for decades. Entire kingdoms of life don’t have introns. So they’re irrelevant to discussions about Prebiotic Earth and the validity of common descent.

    I’m disgusted with myself for hoping that you might engage rationally and for following you down your rabbit hole. This has just been another case of arguing with someone who is ideologically committed to intelligent design, who anomaly-hunts rather than understanding and following the weight of evidence, and who gets their material directly from ID websites.

    The only good that came of it is I learned more about introns.

  73. BillyJoe7on 08 May 2014 at 6:03 pm


    “You didn’t answer the question”

    (The question being: Why would they assume that species further apart on the tree would have more different features and species closer on the tree would share more similar features?)

    You didn’t like the answer.

    (The answer being: they assumed that species further apart on the tree would have more different features and species closer on the tree would share more similar features because, amongst other factors, they failed to consider, or underestimated, convergent evolution).

    “homeopathy works every time someone who takes it gets better”


  74. sonicon 09 May 2014 at 1:48 pm

    You seem to have confused a specific example for a principle.

    The principle I’m talking about is this–
    If one has only one explanation for a certain set of observations, then it turns out that there might be more than one explanation, this reduces confidence in the first explanation.

    Would you agree to that in principle?

    Do you see how the intron, HGT, ‘convergent evolution’, explanations for DNA sequence similarities reduces confidence in the ‘common ancestor’ explanation for those same sequences?

    I realize the DNA sequences is only part of the evidence for ‘common descent’ so I’m not saying that ‘common descent’ is wrong based on this.
    What I’m saying is my confidence in that part of the evidence is reduced because i see now there are other possible explanations for the sequences that have been used to ‘prove’ common descent.


    I don’t really know enough about ‘intelligent design’ to have a ‘commitment’ to it one way or the other.
    Actually, I don’t know how one would define ‘intelligence’ or ‘design’ rigorously enough to even know what we are talking about.
    I did read a book ‘signature in the cell’ which I thought was quite interesting, but I remain unconvinced that there is a theory there at all.

    Did you learn that most organisms, including mammals, have introns?

    You have pointed out what they weren’t considering– not what they were.
    So you haven’t said what they were thinking at all– only what they failed to consider.
    See the difference?

    I said “if one takes only the positive” about homeopathy.
    You’re being a ‘quote miner’.

    Did I use that term correctly? 🙂

  75. grabulaon 09 May 2014 at 9:49 pm


    I’m not interested in providing evidence to you – it doesn’t work. What I am doing is pointing out how bad your line of logic and reasoning is, and where it goes wrong. It’s my belief that that’s possibly the only route through which people like us might reach people like you. This thread is an example, you’ve been given mounds of evidence for the articles topic and been given tons of sound reasoning for why your argument doesn’t amount to discounting current evolutionary models. How do you respond? By continuing to hammer away like a robot at one tiny study you believe provides enough evidence to dismiss current understanding of the evolutionary model.

    “I said “if one takes only the positive” about homeopathy.”

    There is no positive about homeopathy, it’s been shown time and time again it doesn’t work because there’s never any evidence it does. Not only is your reasoning terrible, your examples are as well.

    Honestly I suspect you’re a young earth creationists or something there about hiding behind science that seems in your mind to disprove all of the science that refutes your beliefs. You’ve been purposely obtuse about evidence provided to you. You’ve also maintained a really common tactic for young earthers – picking a tiny variance that indicates something might be contributing and then conflate it to mean the science has been disproven.

  76. sonicon 10 May 2014 at 9:54 am

    You are correct– a small study should not be used to dismiss the current evolutionary model.

    I suggested that if there has been only one explanation for a particular phenomena, and then it is discovered there is more than one explanation for that phenomena, the confidence that each example of the phenomena is explained the first way is reduced.
    The specific example I gave had to do with certain DNA sequences and how certain shared sequences have been considered to be always the result of common ancestry when in fact they might be the result of something else.

    Would you address that? Please?

    Of course numerous people say they have gotten better from taking homeopathic remedies.
    If one were to only consider those statements, then one would conclude homeopathy works.

    Could you agree to that?

    I am not a young earth creationist. LOL.

  77. BillyJoe7on 11 May 2014 at 6:06 pm


    “Of course numerous people say they have gotten better from taking homeopathic remedies.
    If one were to only consider those statements, then one would conclude homeopathy works”

    Only if you are scientifically illiterate.

    “I suggested that if there has been only one explanation for a particular phenomena, and then it is discovered there is more than one explanation for that phenomena, the confidence that each example of the phenomena is explained the first way is reduced”

    Only if you are scientifically ignorant.

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