Weekly reader beefs

July 19, 2014 • 6:46 am

For some reason, most of the non-published comments this week came from evolution deniers, although, as usual, a few trickled in from outraged citizens of Lebanon, Missouri. Here’s a selection of four that didn’t make it to prime time.

Reader “Jimmy” comments on “Baleen whales: a lovely transitional form“:

What a load of old cods!!! With this kind of logic anything can be advertised as transitional, absolute rubbish! There should be literally millions of transitional forms if Evolution is true, why do we not find them? If you cant get past the basic start of life ie life from non-life why do you carry on with this fantasy? Life cannot start with Oxygen present, Life cannot exist with Oxygen present, sort that out! Dont bother replying I will be out back digging up some extinct creature and passing it off as a transitional form somewhat smarter than the average member of the Evolution Church!!

Cheers

We have gazillions of transitional forms; are they all to be ignored or discounted? But really, what is this talk about “old cods” (I suppose he means “codswallop“): claiming that life cannot exist with oxygen present? How does that discount that life started in an anaerobic (oxygen-free) environment and, after evolved forms produced oxygen, had to subsequently evolve in that new environment. Does this person not know about adaptation to environmental change.

This kind of willful ignorance—and it is willful since the evidence is readily available—is what we’re up against in the U.S. I could show Jimmy hundreds of transitional forms, including the feathered dinosaur I highlighted a few days ago—and he’d still reject them all. Any bets on whether he’s religious?

*****

Reader “tom” comments on “What would disprove evolution?

The tree of life is a tidy little concept,intuitive, reasonable,rational, it fully satisfies anyone who has no real interest in thinking much less in verification of fact. In reality there is not even a sniff of proof of any component of the evolution hypothesis. On the other hand anyone who tries to comprehend the sheer statistical probability that a strand of RNA can randomly arrange itself in such a manner as to contain information to build a protein soon comes face to face with cold reality. Ribose is a sugar, an organic molecule which can only be produced by photosynthesis. All attempts to artificially induce its formation have met with failure. To assume this can be realized randomly in pond water is the zenith of stupidity. No attempt to synthesize or induce such synthesis have ever succeeded for any complex molecule associated with creation of a living cell or organism. So given the absence of the most basic components of even RNA, how can a reasonable mind mind conclude it could ever appear via abiogenesis?
Our current understanding of the universe is embryonic at this stage and for people to force fraudulent claims on others as proven science, is a dissevrice to science,and humanity.

Again, we see a flat denial here of evolution—by the same people who gladly take antibiotics whose efficacy is supported by the same kind and degree of scientific evidence that evolution occurred. There’s also the willful and pervasive misunderstanding that the primordial replicating molecule (possibly RNA) “randomly arranged itself.” Of course that wasn’t random: even the original molecules, as Addy Pross shows in his nice book What is Life? How Chemistry Becomes Biology, natural selection had to act on those early precursors, which means that they weren’t assembled “randomly.”

One of the most common tropes of creationists is this: “you haven’t yet created life in the lab yet, and have no idea how it happened.” And yes, that’s a puzzle for the time being.

But I’m pretty sure we’ll be able to create replicating molecules in the lab under primitive Earth-like conditions within a century. What will they say then? Probably this: “Well, you don’t know that it happened that way!” And yes, we won’t, but it doesn’t matter. If we can show that life originated under purely naturalistic conditions, that destroys the creationist argument for God based on the fact that life couldn’t have originated naturalistically.

And beyond that, of course, once it did originate, we have tons of evidence for evolution once early organisms were present. I believe I wrote a book on that evidence.  How do creationists deal with that? I suppose they’d say, “Well, yes, evolution might have occurred after God created the first living thing, but that first thing had to be created.” But no creationist says that, not even advocates of Intelligent Design. They fall back on our present ignorance of how life began only because we have so much evidence that once it did begin, it evolved. In other words, they’re using the origin of life as a god-of-the-gaps argument.

*****

Reader “Brent Dawes” comments on “OMG: a three-ton wombat!

Why Evolution is True?

You have presented Diprotodon as being a giant marsupial wombat the biggest marsupial to inhabit our planet. And yet it’s “descendants” appear to have lost information to the point where they are less than 100cm long. This happened right across Australia where the megafauna mammals were giant compared to their contemporaries today. Overall a loss in genetic information and no proof of evolution what so ever. The same goes for the whole evolutionary “theory” which has revealed no examples of any evolution amongst species ever, only wishful thinking and speculation by “scientists” who are looking in the wrong direction, down, when they should be looking up.

Now there’s a new one one me: a reduction in body size represents a loss of information!? Well, what about those creatures that got larger, like nearly all mammals compared to the early ones? But leaving that aside, I’m not sure how a reduction of body size clearly represents a “loss of genetic information.” It represents a loss of mass. But that loss could It could epresent a gain of information, if a reduction in body size came from the acquisition of new genes.

The canard that evolution has given no evidence for “new genetic information” is, of course, dead wrong, for we have examples of both new genetic information originating in real time (see here for some of that), as well as of historical evidence based on gene duplication, whereby duplicated genes diverge in function and assume new functions. Our different kinds of hemoglobin genes (alpha, beta, gamma, and so on) all do different things, yet all descended from one ancestral gene. There are many such gene families, all descended from a common ancestor and all diverging after duplication to do different things. If that’s not “the origination of new genetic information,” I don’t know what is. We also have the work of my colleague Manyuan Long here at Chicago, and of David Begun at the University of California at Davis, showing that in the fruit fly Drosophila new genes doing new things originate very quickly, and those genes are often cobbled together from other genes scattered throughout the genome. Evolution can do strange things!

And finally we hear this cry from Mr Dawes, equivalent to his saying proudly, “I am ignorant!”: “The same goes for the whole evolutionary ‘theory’ which has revealed no examples of any evolution amongst species ever, only wishful thinking and speculation by ‘scientists.’” (Why is “scientists” in scare quotes? Don’t we exist?) This isn’t the nice kind of ignorance which simply reflects lack of acquaintance with the evidence, but the deliberate and dark kind of ignorance: ignoring the mountain of existing evidence for evolution. It’s not stupidity, but intellectual malfeasance.

*****

Finally, reader “Diest” (somehow I think it’s supposed to be “Deist”) comments on “A warning to Lebanon, Missouri: another state high school successfully sued for promoting religion“:

Why do you even care about what was said? I just want to know how you can you hate God/Gods a different religion so much if you dont believe is true.. If you agree disagree or think God exists or doesnt how can you hate it…. If you dont believe its real or anything is true, how can you disagree with something you dont believe even exists to begin with?

1. Why do I care? Because of the Constitution.
2. I don’t hate God, because you can’t hate something that doesn’t exist. I dislike the idea of God because it’s deceived so many people and thereby promoted a lot of bad things on our planet.

That comment shows that people like “Diest” don’t have the slightest notion of what atheism really is.

 

125 thoughts on “Weekly reader beefs

  1. Every fossil is a transitional fossil. To claim there are none demonstrates a fundamental misunderstanding of the TOE.

  2. Anything can indeed be thought if as transitional. Every living thing past and present represents it’s own point on a continuum.

    And we care about what theists do because the things they do are really being done. An atheist 400 some years ago shouldn’t care about being hauled off to be burned at the stake, because, hey, that atheist doesn’t even think god exists. Why should what theists do matter so much?

    These comments really highlight the trouble with abstract thinking, or at least with dot-connecting, that often accompanies theism.

    1. The trouble is these guys have a rather childish literalism/reification of nouns vis-a-vis the objects the nouns represent. “Bird” is obviously completely different from “dinosaur”, so if you show them a fossil of a transitional species between dinosaurs and birds, the only thing they seem capable of doing is to classify it as either a dinosaur or a bird and therefore not transitional.

      1. Maybe it’s pronounced like diced? As in a quarter cup of Diest Onion. By the Diest logic, to not recognize something is to hate it. I wonder if that means Diest’s writing style betrays a hatred of punctuation marks?

    1. Actually, my first interpretation after ignoring the obvious “illiterate fool” explanation was that the author was also an anti-vaxxer or faith healer. Both show a tendency to die sooner rather than later and for pretty much the same reason why creationists still exist (arrogantly willful ignorance).

  3. “I’m not sure how a reduction of body size clearly represents a “loss of genetic information.” It represents a loss of mass.”

    You just have to look at the computer industry – all that miniaturisation has meant that today’s computers aren’t nearly as powerful as the big ones we had in the pas…oh! no, that doesn’t seem to work! 😉

      1. There WAS plenty of “information” lost in the megafauna extinctions in Australia and elsewhere [always, curiously, upon the arrival of humans, so must have been part of god’s plan].

        But it’s pretty clear that Brent and his bros read “wombats were giant once” to mean “then they became little” rather than “wombats were once very diverse but we ate all the big slow juicy species”. This understanding is much like the “why are there monkeys” — I think fundamentalists have no problem with evolutionary change but can’t grok phyletic splitting.

  4. Now there’s a new one one me: a reduction in body size represents a loss of information!?

    Correct me if I’m wrong, but isn’t the current record-holder for the largest (vertebrate?) genome is something like a salamander. And some protozoans have remarkably large genomes too.
    Someone – the original author – is deficient in knowledge.
    I suppose it’s not unreasonable to think “big animal, lot of information needed to build it”, but it really doesn’t work like that. It’s somewhat counter-intuitive, but intuition isn’t necessarily correct.

    1. Everybody knows that intuition increases with body size.

      And memory.

      That’s why elephants and whales never forget.

      QED

      1. But … but … that would mean that baby whales don’t have very good memories, which would imply that teenage (middle-size) whales wouldn’t have anything to remember as their memories improve.
        No?

        1. Maybe the teenage whales fabricate their memories just like creationists fabricate their ‘facts’.

            1. Dang. Even googled it.

              I thought a small group was a pod and a large a school.

              Only for fish, then?

              1. It’s not really something that I know much about. It’s just that every New Zealander around my age (50) knows that one because it was on the first page of primary school maths texts as part of the lesson on sets. 🙂

              2. Yes, sets are often used as a way to manipulate young minds. What started as ideas espoused by a group of unemployed scholars morphed into a period of great social and political upheaval culminating in the terrible reign of Venn.

              3. I had to wiki him. 🙂

                And am now left wondering if I skipped those math-lessons or if I need to gain weight.

              4. “By gum”, thought the publishers, “we’ll ensure every child in New Zealand not only understands sets but also knows what a bunch of whales is called!”

                😀 🐳🐳🐳🐳

              5. “And am now left wondering if I skipped those math-lessons or if I need to gain weight.”

                LOL!

              1. Maybe this is why New Zealanders are so big on saving the whale! Our country takes on Japan in the international courts to stop whaling with multi-partisan support. We spend multiple millions on it and there are only 4.4 million of us. And it all started with indoctrination in primary school! Who knew! 🙂

    2. Yes. The genome size does not correlate with complexity, nor with the amount of genetic information, i.e the # of genes. The onion Allium ursinum has ~ 9 times more DNA than the human genome, but most of that DNA is not for genes. Most of our DNA is not for genes as well. I accept the evidence that most of this DNA is ‘junk’.

      1. I accept the evidence that most of this DNA is ‘junk’.

        I’ve never liked that term. Granted, we don’t know what much DNA does, but we do keep on finding new things that DNA does do in terms of regulatory elements, structural controls (making different pieces of DNA appear on different parts of the coiling and super-coiling of DNA strands, affecting it’s expression).
        “Non-coding DNA” is a far less pejorative term, which is also less likely to be wrong.
        I just have this nagging suspicion that by using a pejorative term like “junk DNA”, we’re setting ourselves up for a pratfall. It’s a rod for our own backs, which our enemies across in the Creationist camp are going to pick up one day.
        Well, they do try already, though somewhat hampered by their overwhelming sheer, bloody-minded ignorance of the subject. But I still don’t like leaving them rods, for breaking over our backs.

        1. As far as I understand it, the one that came up with the idea (Ohno?) of previously used DNA (pseudogenes) et cetera was not using the term in a pejorative sense. It wasn’t “crap” DNA but “junk” DNA, recyclable (and indeed sometimes recycled) as the junk stored in an attic.

          Genomicron is a blog from a specialist delving into some of that history, and if memory serves so do Larry Moran @ Sandwalk.

          1. Oops. I meant that the originator of the model lumped together elements, not necessarily discovering or suggesting them. Those elements were likely known since earlier.

          2. Hmmm, it was Ohno (sorry, but that name has got to be spelt with an exclamation mark, always), was it? I remember encountering him in the “plastic-eating bacterium” work – as light entertainment from studying chronic H2S poisoning. I didn’t know he’d been working that far back.

        2. I suggest that you look at Larry Moran’s posts at his Sandwalk blog over the last few months. In summary, about 1-2% of the human genome is transcribed into proteins, about another 8% has some other functions, but at least 50% is all sorts of parasitical rubbish that is known to have no function for our survival: junk. Of the other 40%, it is probable that a little might have some relevant function, but most of it is likely to be further junk.

          1. Not knowing what something does is not the same as knowing that something does nothing. We’ve only been studying DNA for 2 generations or so. Claiming that we know what it all does is (1) almost certainly flat-out wrong and (2) hubris of an order that would attract the violent and sarcastic attention of the Greek gods, if only they existed.
            I’ll put on my copper-plated boots and lightning conductor hat now.

            1. We know for a fact that certain sequences of human DNA are leftover from ancient viral infections, and that other sequences are duplications. For example, I believe we have five copies of the gene that in other species synthesizes vitamin C, but none of our copies work. I’d say that qualifies as junk.

        3. The term ‘non-coding DNA’ is already taken to refer to all DNA that does not code for functioning RNA. It includes what is referred to as junk (pseudogenes, inactive provirus DNA, inactive transposable elements, and other stuff) plus DNA that has function but does not code for functioning RNA. These include gene regulatory DNA, centromeric DNA, and maybe telomeres.

          What is called junk DNA is sometimes recruited to be functioning DNA, but so far it looks like that as happened only to a very very small % of it. There is no hope that the rest has function in a way that we currently know about.
          Maybe the term ‘junk’ is not so great, but there are lots of terms that are similarly awkward. ‘Pseudogene’ is a lousy term for a formerly working gene that is now mutated to the point where it does not function, so I agree that we might look for a better term.
          The balance of evidence is so far/i> pursuasive that junk DNA on the whole has no function. I agree we should still hold a final, carved-in-stone judgement on that, however. For example, maybe some of it has a role in providing generally useful architecture for chromatin in the nucleus.

          1. “The term ‘non-coding DNA’ is already taken to refer to all DNA that does not code for functioning [messenger] RNA.”

            Your definition of non-coding DNA only works with my edit in square brackets above. Ribosomal RNA, transfer RNA, other functional RNAs that do not code for the amino acid sequences of polypeptides/proteins are non-coding DNA as well.

  5. Lovely comments those are. I used to do videos on YouTube about atheism, religion, evolution, and so on. I got bored of the same arguments that have been refuted so many times by so many people.

          1. And if you look on a list from a meatpacker, you’ll find pizzles (bull penises). Dang things are LONG! Very sinewy, they’re used mostly for dog treats, but also for walking sticks. (A metal rod is run thru the middle.) How do I know stuff like this? My friend Louis Greenwald, a meat wholesaler, once ordered one for a customer.

            1. I just don’t see the attraction of owning & using a bull penis walking stick….so, I dunno, I want to say “pervy” but I just don’t know how to classify my aversion to such a thing.

              1. Yep, not on my list of desired accessories, either.

                And I don’t think it’s what Gid Tanner or any of the many others who have covered this one have in mind, either.

              2. I’m unable to come up with something to say here that doesn’t involve the phrase “polishing your walking stick.”

            2. Without my walking stick, I’d go insane
              I can’t look my best I feel undressed without my cane
              Must have my walking stick ’cause it may rain
              When it pours, can’t be outdoors without my cane

              If I ever left my house without my walking stick
              Well, it would be something I could never explain
              Oh, the thing that makes me click, on lovers lane
              Would go for naught, if I were caught without my cane.

  6. I would bet my own money that the last one has never been a minority anywhere. Cases like Lebanon and Fayette are wrong because it is deliberately making those who aren’t Christians feel less than. Private citizens can do that all they like, but public officials have a responsibility to treat everyone fairly. It’s harder for kids to get an education if they have to worry about their teacher belittling them for their or their parents’ religious beliefs.

    (Hell, the Fayette case isn’t even about atheism directly; IIRC, the family was Buddhist. But sectarianism can affect us all, even if this case was brought by a Buddhist, I imagine that atheists, other religious minorities, and even those Christians who don’t have a problem with evolution were happy with the decision.)

    1. Yesterday I aggravated one of my creationist antagonists at gocomics, who had stated that there is no such thing as evolution, by asking him to refute the so-called “germ theory” of disease.

  7. It’s utterly baffling to me how creationists continually cry foul at the facts of evolution but think that their obvious fairly tale holds up at all. The story in Genesis is absurd, particularly the bit where the supposedly all wise god puts the tree of knowledge in the Garden of Eden. Uh, why does god need a “tree of knowledge” and why, given he could have put that tree anywhere in the whole wide world, or anywhere i the universe for that matter, he put it in the very garden with the people he didn’t want to munch on any fruit from that tree. That’s either a verrrrry stupid god or a very conniving god and even if that particular god did exist, I wouldn’t worship him and while I might fear him due to his immense power, I certainly wouldn’t respect him for decency or intelligence.

    1. It’s utterly baffling to me how creationists continually cry foul at the facts of evolution but think that their obvious fairly tale holds up at all

      I’ve highlighted the error. They don’t think. At least, not in any coherent and wide-ranging way.
      Seriously, at some point in their mental process, they just disconnect. Even quite intelligent ones otherwise get to some point in the discussion and BZZZZT : short circuit, end of discussion, jerk of the knee.

  8. Our current understanding of the universe is embryonic at this stage…

    And religion is abortion.

  9. ” If you dont believe its real or anything is true, how can you disagree with something you dont believe even exists to begin with?”
    ___

    As soon as someone mutters god, I correct them, and say, you mean your god belief, don’t you? Allowing the focus to be on god itself automatically gives credence to its existence.

  10. Diest is a town in Flanders, and consequently Van Diest (“of Diest”) is a somewhat common surname in Flanders and the Netherlands. Some of them have found their way to the US. This may or may not be relevant to this particular commenter.

    1. YES, and what is interesting about that is summarized in your link (key line in bold):
      “…the pentose phosphate pathway appears to have a very ancient evolutionary origin. The reactions of this pathway are (mostly) enzyme catalysed in modern cells. They also occur however non-enzymatically under conditions that replicate those of the Archean ocean, and are then catalyzed by metal ions, ferrous iron Fe(II) in particular. The origins of the pathway could thus date back to the prebiotic world.

      1. Ah, they added Keller et al to Wikipedia! The letter that accompanied that paper in Mol Syst Biol pointed out that there are ways to drive that equilibrium chain backwards, from pyruvate to glucose/ribose, say by membranes separating product from catalyst.

        I am no expert here, but I think it is interesting in the context of prebiotic metabolism and RNA both.

        First, this wasn’t supposed to happen. The possible side reactions should spread products all over the possible molecules. But chemists couldn’t model the thermodynamic process, and it turns out the primordial chain (if that is what it is) is as efficient as the modern, at some 25-30 % end product. Just much slower.

        Second, there have been many suggestions of carbon uptake root autotroph metabolisms, of which the most promising ones stops at acetyl. (Promising in the sense that they share traits with today’s metabolisms.) The 2 carbon (acetyl) to 3 carbon (pyruvate) bottleneck show up even today, with many ways to bridge it. (Including such that reminds of the proposed acetyl chains.)

        Third, it is just a hop, skip and jump between glucose and pentose and pyrimidine RNA nucleotides. They even do the metal catalyst trick, but with the modern Mg2+ that seems to be just shy of Fe2+ efficiency in an anoxic world. (I believe the idea is that Earth oxygenation made cells evolve Mg as substitute for the then problematic Fe in enzymes.)

  11. You mentioned the Addy Pross book above. Are there additional good books on the subject that you (or anyone) can recommend? I see there is one by Peter M. Hoffman titled Life’s Ratchet: How Molecular Machines Extract Order from Chaos. I wonder if anyone here has read that one.

      1. Thanks. Will check it out. I’ve seen Hazen’s lecture series on science in general on The Great Courses. He’s very good.

      2. Hazen’s book is excellent, and well worth reading, but only seven years later it is already out of date, so fast is the work on abiogenesis proceeding. As someone with a physics background I think that Hoffman’s Life’s Ratchet is absolutely brilliant. Amongst other things, it utterly destroys the creationist rubbish about the second law of thermodynamics being a problem for biology.

      3. Yeah, I read that one a couple of years ago. Bob Hazen does a couple of good “Teaching Company” series of lectures too.

    1. I would also recommend the book by Pross. It is surprisingly short, but he is an excellent writer. I flew through it.

      1. I agree on the value of Pross’s book, but disagree on the excellence of his writing, which I found annoying. He’s constantly telling the reader how amazed we’re going to be by what he’s about to say next, and how he’s solving problems that have stumped scientists for decades — when in fact much of what he says is stuff I thought fairly obvious and uncontroversial. I think he’s done a service in bringing it all together in an accessible format, but it’s not nearly as groundbreaking as he makes it out to be, and I would have liked it better without the breathless self-congratulation.

        1. Or just remove the “http://” from the link. WordPress will add it back but not embed the picture (or video).

      1. Thank you! I am maybe a bit more educated in these things than TCMITS but this could still be interesting!

  12. I love these weekly reports from the deluded.

    Just before I read this I told a guy on Twitter that the life sciences only exist BECAUSE evolution is true. Here’s his response (two responses condensed into one):

    “It’s a fallacy to say the life sciences depend on evolution being correct. Only theories about origins are affected. Like many lying evolutionists today, you ignore the distinction between historical and operational science.”

    1. Ha ha! The “historical” science canard again! We’ve heard this from Ken Ham ad nauseam.

      1. There actually is such a thing as historical science, though there isn’t such a thing as operational science. The distinction is between historical and non-historical. Any science that investigates events in the distant past based on the traces they have left in the present is historical: much of geology and astronomy, paleontology, biogeography, comparative biology, and phylogenetics, both molecular and morphological. Non-historical sciences investigate either timeless, universal phenomena or events in the quite recent past that we can tell ourselves are “now”.

        1. Creationists warp what historical science is, however, and focus on evolution and abiogenesis.

          I also find that term in general annoying anyway. I know I’m being pedantic, but history is about the recorded events of humans and those sciences predate humans. It’s like thinking archaeologists deal with dinosaur bones.

        2. I would add that the study of evolution is largely a historical science. And… nothing in (operational) biology makes sense except in the light of it. I know one can rightly object to that, but it is still true that our understanding of life is incomplete without understanding its history.

    2. you ignore the distinction between historical and operational science.”

      Utter claptrap. Codswallop too.
      I’m an operational scientist who steers oilwells to their target using tools based profoundly on that “historical science” of evolution (specifically, palaeontological dating).
      The correspondent really does not know what he’s talking about. But we knew that already.
      As Wolfgang Pauli said (in German), “Not even wrong.”

  13. …for people to force fraudulent claims on others as proven science, is a dissevrice to science,and humanity.

    Translation: To force me to look at the mountains of evidence supporting the inescapable conclusion that life evolves under the influence of natural selection hurts baby Jesus.

  14. These posts are always a favorite for me. But i am not confident that modern wombats descended from really big wombats. It seems a bit more likely that the big ‘uns were an evolutionary dead end, and that our modern wombats are descended from a smaller species.

    Wombats are a nice example of highly modernized convergent evolution upon the American woodchuck. Besides resembling them, wombats also dig up your vegetable garden, eat everything in it, and are most often observed as roadkill.

    1. Your description of wombats remind me of the inevitable fate of creationist letters, as demonstrated by Jerry.

  15. I’m not sure how a reduction of body size clearly represents a “loss of genetic information.

    Why, it’s the loss of the information needed to get big, of course. And an increase in size is loss of the information needed to stay small. All evolution is loss of information, if you think of it right.

    More importantly, there hasn’t actually been an evolutionary reduction of body size in Australia. The giant wombat isn’t the ancestor of modern wombats. It’s just that the biggest marsupials were more vulnerable to extinction at some point in the not too distant past. (Through human intervention? Climate change? No idea.)

    1. “(Through human intervention? Climate change? No idea.)”

      Australia’s tricky like that: too flat and geologically inactive to have a continuous fossil record, and both megafaunal extinction and human arrival are beyond useful C14 range. Doesn’t mean people don’t build careers on fighting over the question though. I’ve seen’em get up in professional meetings and tear into an undergraduate speaker who referred to the other side’s papers…

      Giant wombats (Phascolonus etc.) are indeed not ancestral to extant species, and Diprotodon is in a completely extinct vombatimorphian family – no closer to modern wombats than koalas or thylacoleonids.

    1. With the recent Keller et al result on the abiotic glycolysis/pentose phosphate pathways (discussed above), I find the -09 synthesis roundabout pathway less likely.

      With Keller et al you have all the necessary starting material, the modern metabolites to boot, from just pyruvate and phosphate. (And admittedly a separation process, but Russel, Martin et al are already suggesting that on the way to pyruvate.)

      But it is an excellent example of how creationists haven’t bothered with the very science they attempt to criticize! It is 5 years already…

  16. I’d make a somewhat different response to our current lack of understanding about how life first evolved.

    Evolution happens. No matter how life began, it evolves. Even if God created earthly life at some point 3+ billion years ago (which I don’t believe), we have abundant evidence that life evolves.

    We are making inroads in the difficult mystery of life’s origin. We have good reasons to think that the whole process is natural. Hopefully some day we’ll understand how it can happen.

    And then I might deal with some details, like the oxygen thing, and the fact that life didn’t start in open water of lakes or pools and . . . (There was a lot of error condensed into those paragraphs.)

    1. I think the most obvious reason for it to be a natural process as everything else is that the Hot Big Bang inevitably made a universe without life and now we observe life.

      Natural processes would not be possible if life somehow preceded or was concurrent with the universe. But we see that it originated within the universe, similar to how chemistry and geophysics, life’s roots, did.

  17. Life cannot start with Oxygen present, Life cannot exist with Oxygen present, sort that out!

    How hard can it be to look up when Earth was oxygenated, which is both a geological observation on its own and a result of previous life, and the earliest splits in TimeTree and find out that life predated oxygenation with at least 1.3 – 1.8 billion years? Life could have existed as long without oxygenation as with!

    The early history here seems to shake out well by the way. The earliest accepted fossils date to 3.5 Ga bp (billion years before present). There are at least two independent claims of fossils in the little metamorphosed Isua formation at 3.8 Ga bp, but it doesn’t seem to be widely accepted. It is promising though.

    And now they have found evidence for a prototype craton in the more metamorphosed Acasta formation at 4.02 Ga bp. (Which morally and practically is Hadean.) The Icelandic type rocks seems to predate early but immature craton TTG rocks. They claim evidence for mid-oceanic ridges. (Even though the craton emergence is connected to mantle upwellings.) Presumably older plates were shortlived oceanic, today ~ 100 million years average lifetimes. Hence the oldest 4.2 Ga bp Acasta rock material, and the absence of older evidence, is neatly predicted.

    So maybe life, and craton material, survived the late bombardment spike 3.8 – 3.9 Ga bp. Even with the less energetic Nice 2 model. That model marries the old Nice model for our planetary system with recent exoplanetary system formation models (and nicely predicts the outer moon behavior). [Wikipedia.]

    Given that model the same initial impact mass flux from the original protoplanetary disk is seen at ~ 4.35 Ga bp. That is 50 million years shy of the oldest known zircon that now has been verified attests to a cool early Earth at 4.4 Ga bp. The absolute earliest possible date for life would not be much older than 4.45 Ga bp, which is the current best date for the Moon impactor.

    FWIW to convince creationists about the consistency of science findings, the Timetree date for the oldest dated splits at 4.3 fits within these time frames. Whether or not the preceding universal common ancestry lineage go back a further 50 or 100 or even 150 million years.

    after evolved forms produced oxygen, had to subsequently evolve in that new environment.

    The root of the enzymes that prevent local damage from the OO (O2) oxidant seems to have evolved to handle the even nastier NO oxidant. NO2 is believed to have existed in biologically relevant steady state concentrations before the oxygenation, produced by CO2 and NH3 around volcanoes (or impactors early on).

    This is of course independent evidence for the anoxic-oxygenated transition. And evidence that for life to survive the global oxygenation was not too much of a stretch!

    1. The early history here seems to shake out well by the way. The earliest accepted fossils date to 3.5 Ga bp (billion years before present). There are at least two independent claims of fossils in the little metamorphosed Isua formation at 3.8 Ga bp, but it doesn’t seem to be widely accepted.

      Some slightly creaking ice there. Schopf’s claim of the 3.5Ga fossils was savaged by Brasier about 8 or 10 years ago. TTBOMK, Schopf hasn’t come back with anything better, and nor has anyone else. So the current generally-accepted oldest fossils are around 3.3Ga old, not 3.5Ga.
      Mojzis’ claim to have a biogenic signature (highly negative delta-13C) on graphite flakes in apatite crystals from the Isua Supercrustal sequence, (“Evidence for life on Earth before 3,800 million years ago”. Nature 384 (6604): 55–9) is considered quite controversial and not generally accepted, not because people suspect he’s got his techniques wrong, but because there’s a lot of possible conflicting or complicating factors. These are rocks with very long and complicated histories.
      On the other hand, the Late Heavy Bombardment may not have been such an issue ; even if you boiled off 75% by volume of the ocean in a major impact, you’d still leave plenty of water depth over the (probable) site of the origin of life in hydrothermal systems. So the “drive” to fit the origin of life into the gap between LHB and Schopf’s (dodgy) 3.5Ga claim is less constraining than we were feeling a few years ago.

      1. Thanks for the response!

        – Yeah, I never liked Schopf’s results. And I like Brazier’s paper.

        – There have been several independent claims of 3.5 old bacterial formations along the lines of Brazier, if memory serves Brazier et al own later result, but especially Hazen’s et al Dresser formation MISS among them. I haven’t heard any criticism of either, so I assume they are admitted, especially since everyone continues to quote 3.5 rather than 3.3 Ga. [Hazen et al: http://www.astrobio.net/news-exclusive/the-oldest-signs-of-life-on-earth/ ]

        – I wasn’t referring to Mojzsis, precisely since they are controversial and for good reason. There are two recent microanalysis results that can be of better value, and have less problems with competing hypotheses.

        1. “Biological Fe oxidation controlled deposition of banded iron formation in the ca. 3770 Ma Isua Supracrustal Belt (West Greenland)”, Andrew D. Czaja et al, Earth and Planetary Science Letters 2013; http://www.sciencedirect.com/science/article/pii/S0012821X1200711X .

        “Although these BIFs have been metamorphosed to amphibolite-facies, the metamorphism can neither explain the range in Fe isotope compositions across bands, nor that between hand samples. The isotopic compositions therefore reflect “primary”, low-temperature sedimentary values.”

        “A dispersion/reaction model, which accounts for rates of hydrothermal Fe(II)aq input, rates of oxidation, and rates of Fe(OH)3 settling suggests exceptionally low O2 contents, <0.001% of modern O2 contents in the photic zone. Such low levels suggest an anoxygenic pathway is more likely, and the data can be well modeled by anoxygenic photosynthetic Fe(II) oxidation."

        2. "Evidence for biogenic graphite in early Archean Isua metasedimentary rocks", Ohtomo et al, Nature Geoscience 2013.

        A little more like Schopf perhaps, but they can exclude abiotic formation, at the metamorphic temperatures, of the carbonaceous material structures.

        I don't know the status of either. Which, I guess, is telling. The Keller et al pentose paper was encyclopedic very shortly…

        – LHB: The latest model of Abramov et al, compatible with Nice 2, reinserts a 50 % likelihood ocean evaporator impact event. On the other hand they show that with the latest geophysical models the upper crust itself was an excellent refugia, since it never got up to boiling temperatures on average.

        So I have no worries, personally. I was trying to extrapolate their LHB mass fluxes to the initial roughly exponential drop from the remaining protoplanetary disk, the Early Heavy Bombardment if you will. Merely to see what the minimum open period for life emergence is re impactor mass fluxes.

        1. hmmm, I think I saw Ohtomo et al’s work when I briefly had access to Nat.Geosci. last year. The Dressler stuff is new to me though.
          I’ll have to have a trawl through that Astrobio magazine.

  18. What I really love so much about evolution deniers is that everything, even me, are transitional forms which they, of course, deny.

    1. I do not think we can use the term for ourselves, since we do not represent an ancestor of any species.
      The term ‘transitional form’ is usually applied to extinct species that are members of a group that has left descendants. Although we generally do not claim that the extinct, transitional form species is a direct ancestor to any species alive today. They serve as proxies to the ancestor species, giving us an idea of what an ancestor might look like.
      Some do use the term for modern, living species that in some way resemble what a possible ancestor might look like. I personally do not like it when this is done, but it is done anyway.

      1. We’re transitional forms if we have any descendants.

        Most creationist claims are actually denials of ordinary reproduction (which includes common descent). The only other things they deny are abiogenesis and the Big Bang.

        Denials of natural selection are logically empty and self-refuting, so I don’t even count that.

  19. Reader ‘Jimmy’ needs to learn about the evolution of language too. The meaning of “cod” in “codswallop” is male genitalia, so you can use your imagination as to what codswallop literally means. Surely that’s not suitable language for a respectable creationist?! 🙂

  20. Listen to this weeks Radio Lab podcast. They take a trip to the Galapagos and discuss the changes since Darwin’s visit. Including the evolution of a new finch species as a response to a new flea larvae parasite that is decimating existing species. We may be observing “macro” evolution in real time.

  21. “That comment shows that people like “Diest” don’t have the slightest notion of what atheism really is.”

    And, possibly more to the point, it shows that they have no idea what Christianity is to non-Christians, no awareness of how bullying and degrading to others Christians often are. They think that if they are only degrading and bullying a minority it doesn’t count.

  22. On the other hand anyone who tries to comprehend the sheer statistical probability that a strand of RNA can randomly arrange itself in such a manner as to contain information to build a protein soon comes face to face with cold reality. … To assume this can be realized randomly in pond water is the zenith of stupidity.

    What people can see of the best pathways is that it wasn’t random, and it was under thermodynamic constraint and even forcing rather than pure “pond” (soup) models.

    But moreover, it seems pretty clear that the initial genetic machinery didn’t evolve to produce proteins. There is a very interesting analysis of the ribosome out in PNAS EE. [“Evolution of the ribosome at atomic resolution”, Anton S. Petrov et al; https://ww2.chemistry.gatech.edu/~lw26/bPublications/LDW_102.pdf ]

    It is consistent with earlier “onion” type models of the ribosome through the accessory proteins to the preserved peptidyl transferase center, but uses a fingerprint of RNA insertion to more or less fully constrain evolution. And evolution it is! The common core has an initial 5 phases out of a total 8 where the translocation (protein decoding) function evolved. [Ibid, pp 4-5.]

    According to these findings the ribosome started out as a generic RNA catalyst site that could do peptide bond formation (the P region). The function could simply been to produce dipeptide catalytic cofactors from tRNA ancestors bound to amino acids. Evolution glommed on pieces that started to support a ridge and eventually a tunnel stabilizing region.

    Later evolution involves an exit pore and an accessory tRNA binding site (A region), indicating that random prolonged polypeptides could have a function, say as 5-6 mere “nests” anchoring catalyst metal sites. (I’m not a chemist, but I suppose the polymer could eventually detach from the last tRNA support by hydrolysis.)

    After tunnel elongation a small ribosomal unit (SSU) docking region evolved. That implies the tRNA have evolved an antisense site and started to produce more useful proteins from mRNA string templates, which was later more securely locked by the SSU. Eventually an energy driven translocation function and E site evolved, perhaps as a means to ensure fast and less varying protein production.

    FWIW re creationists:

    One can put this into the frame of the spontaneous pentose metabolism under 70+ degC hot, anoxic Fe2+ Hadean water. Such a system could have evolved around Hadean submarine alkaline hydrothermal vents. (The recent Acasta finding of early marine plates discussed in an earlier comment indicates those geological structures were around in the Hadean.) That could have evolved pyrimidine metabolism from available starting materials.

    While pyrimidines initially could go into energy/transport cofactors (ATP et cetera), they could also polymerize in the vents by PCR through convection and thermophoresis. [“Thermal Trap for DNA Replication”, Christof B. Mast and Dieter Braun, Phys Rev Lttrs; http://www.biosystems.physik.uni-muenchen.de/paperpdfs/mast_reptrap.pdf ]

    What is lacking is a polymerase. Interestingly, modern polymerases/replicases have a preserved Mg2+ active site, mirroring the ancient anoxic, hot Fe2+ theme of the spontaneous pentose pathway. Two Mg2+ are coordinating the polyphosphate handling, but only one is needed for the catalysis so presumably it could happen. Pity the paper didn’t study that!

    Short RNA chains are useful in various ways, so I presume there could have been a selection for function in the competition for nucleotide use. When you hit replicating strings that are 120ish long, the 116 mer protoribosome becomes possible. And it had only grown to 260ish meres at the time it could translate mRNAs and constitute a genetic machinery resembling our modern ones. It was perhaps 275 meres long at the time DNA genetic storage evolved, which I hear happens in models of parasitic pressure. Separation of replication and translation makes the system more robust. If so viruses had evolved at this time too.

    Interestingly there is non-random evolution and replication out of geophysical systems in such a pathway. (Of which initial amino acid production is left at reader’s digression.) Very little “random arrangement” but a lot of later contingency would be involved.

  23. The faithful are the best unwitting absurdist comedians in the World. You have to love the haughtiness of it all. For instance, IDers and literalists think science is a “fantasy” or “the zenith of stupidity.” The bible has a talking donkey in it. If they have so casual a relationship with objective reality that they would subvert documented scientific fact to a book with a talking donkey in it, it begs the question, do they think of the Shrek movies as some kind of nature documentary? Are they watching on blu-ray, waiting for the moment when David Attenborough explains why the cat is wearing boots? A biblical literalist once asked me to provide evidence that the story of Jonah and the Whale is not true. “Because he was inside of a whale and didn’t get digested, NEXT.”

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