Sunday, 17 August 2014

Abiogenesis - The Day of Reckoning For Creationists is Nigh

Meet your maker: Homing in on the ancestor of all life - life - 12 August 2014 - New Scientist

Creationist pseudo-scientists have a problem, and not the obvious one of more and more people seeing through their deceptions, working out why they are necessary and realising a rational, scientific explanation is preferable to a magical one which requires lies and misinformation to promote it. The problem they have is, like the problem of the virtual certainty that at some point in the near future, scientists will find evidence of life on another planet, probably in another planetary system, the problem of one of their fundamental arguments being shown to be without any foundation.

I'm talking about the fact that science is getting closer and closer to working out how an early self-replicating molecule arose and gave rise in turn to a self-replicating structure capable of extracting energy and using it to manage entropy - in other words, something we call 'life'.

At that point, of course, creationism's imaginary magic creator will have been evicted from yet another gap and science will have shown there is no need to invoke magic to explain life, either on Earth or on any other planet. The entire thing will have been shown to be the result of a natural process involving nothing more than chemistry and physics obeying fundamental laws and, more importantly, inevitable in the circumstances in which it occurred, just as life's diversification and evolution has been shown to be.

An article by Michael LePage in New Scientist a few days ago hints that science may indeed be getting close to that dreaded day of reckoning for creationism.

The problem they may have explained is how one of the most fundamental processes of living things could have evolved. This is a process that must have been present in the last universal common ancestor (LUCA) - a notional organism from which every living thing is descended - because it is fundamental to every form of life. It is the manufacture of ATP from ADP and phosphate. ATP acts as an energy store which can be used to power metabolic processes by reducing it back to ADP and phosphate, so releasing the stored energy to power the process. Energy being added to the system from outside is why life is an open system and is thus able to bring about greater order (reduced entropy) in full accord with the second law of thermodynamics - despite the creationist pseudo-scientists' lie that this is impossible.

The key to the process is a cell's ability to control the concentration of protons inside the cell by using a proton pump to pump protons from inside the cell to the outside. This sets up a proton concentration gradient which can be utilised by allowing protons to flow back into the cell through a protein embedded in the cell wall which produces ATP in the process. The presence of protons in a solution is what we call it's acidity so what this means, in effect, is that the cell needs to be less acid inside than the liquid medium it lives in.

Michael LePage explains this with a simple analogy:

To understand it in energy terms, think of a double kitchen sink. The small sink represents the inside of the cell and the large one the outside world. Start by filling the large sink with water, leaving the small one empty. The difference in water levels is a potential source of energy: drill a hole in the divider and water will flow into the small sink. The flow could be used to turn a tiny turbine – which is essentially what the ATP-making protein is, a turbine turned by protons and other positive ions.

Michael LePage, Meet your maker: Homing in on the ancestor of all life; New Scientist 2982, 12 August 2014

This, of course, requires a membrane impermeable to protons because, in Michael LePage's analogy, if the water can flow back into the large sink both sinks will eventually reach an equilibrium and there will be no flow through the turbine. It used to be thought that LUCA must have had an impermeable membrane for this process to have evolved but, since the realisation that archaea, whose presence was not appreciated when this model was proposed, have an impermeable membrane alright but one which achieves impermeability in an entirely different way to bacteria. This would mean another impermeable membrane evolved AFTER the proton pump evolved if this evolved in LUCA or before. But, what would be the driver to evolve a different way of doing something that was already being done?

Something here is not adding up. The proton pump is common to both archaea and bacteria yet they have different impermeable membranes neither of which could have evolved from the other. The only conclusion then is that the proton pump evolved BEFORE the impermeable membrane. In which case, how did the cell maintain a proton concentration gradient across the membrane?

This has lead biochemist Nick Lane of University College, London, UK to propose that LUCA did not have a semi-permeable membrane; in fact it must have had a leaky one.

For this to work, Lane argues that living cells must have evolved the proton pump/ATP solution around alkaline hydrothermal vents on the sea floor. This had earlier been proposed to explain why living cells use the proton pump and ATP in the first place. As well as being rich in catalysts like iron and sulphides capable of catalysing the formation of large organic molecules like lipids, proteins and, critically, RNA, there would have been natural proton gradients between the acid sea water and the alkaline water flowing up from the vents and out through the porous 'chimneys' which formed as the minerals precipitated out when the hot solution met the cold sea water.

Lane, and his colleagues Andrew Pomiankowski and Victor Sojo have worked out a scenario and modelled it to show that a leaky membrane in just such an environment could be capable of producing enough energy continuously by exploiting the proton gradient across the cell even IF the cell membrane was leaky. This would mean there was plenty of time for these cells to gradually evolve proton pumps and then impermeable membranes, once in archaea and again in bacteria.

Author Summary*

The archaea and bacteria are the deepest branches of the tree of life. The two groups are similar in morphology and share some fundamental biochemistry, including the genetic code, but the differences between them are stark, and rank among the great unsolved problems in biology. The composition of cell membranes and walls is utterly different in the two groups, while the mechanism of DNA replication seems unrelated. We address a specific paradox, giving new insight into this deep evolutionary split: membrane bioenergetics are universal, yet the membranes themselves are not. We resolve this paradox by considering the energetics of a hypothetical last universal common ancestor (LUCA) in geochemically sustained proton gradients. Using a quantitative model, we show that LUCA could have used proton gradients to drive carbon and energy metabolism, but only if the membranes were leaky. This requirement precluded ion pumping and the early evolution of phospholipid membranes. We constrain a pathway leading from LUCA to the deep divergence of archaea and bacteria on the basis of incremental increases in free-energy availability. We support our inferences with comparative biochemistry and phylogenetics, and show why the late evolution of modern membranes forced divergence in other traits such as DNA replication.

In summary then, it's beginning to look as though life developed slowly, not quite in Darwin's "warm little pond" but in the scum forming naturally on a hot little sea bed.

So the day of reckoning for creationists moves a little closer. Somehow between now and then they are going to have to think up a way to explain why a completely natural process is unnatural and why it still requires magic, and they are going to need to start to soften up their victims and prepare the ground for this explanation. I would be astonished to learn that the best brains in the Discovery Institute have not been put to work on this 'problem' already, just as they almost certainly will have been on the impending 'problem' of explaining away life evolving on another planet. Either way, they are going to have to do a lot of creative reinterpretation of the Bible, redefining 'life' and possibly redefining 'intelligent design'.

Either that or they will attack the scientists, lie about the science, deny the evidence and continue as they have till now to rely on the ignorant incredulity and arrogant cultural assumption of their victims that the superstition they were born into simply can't be wrong, and just put up with the inevitable continuing loss of support as more and more people see through their deception and opt for rationalism over Bronze-Age superstition.

*© 2014 Sojo et al. Reproduced under the terms of the Creative Commons Attribution License.

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  1. This blog article is a bit too complicated for me to understand fully, but nevertheless I think I understand the conclusions drawn.

    I did a Google search (prebiotic + membrane + proton pump), and then I found this article from 2009: (Co-evolution of primordial membranes and membrane proteins).

    A quote from that article: The present scenario describes co-evolution of (i) lipid bilayers, – from leaky to proton-tight, (ii) membrane proteins – from amphiphilic, pore-forming ones to highly hydrophobic integral membrane proteins and (iii) membrane bioenergetics – from the relatively simple, sodium-dependent form to the sophisticated proton bioenergetics. The scenario favours the primitive, “porous” membranes as an intermediate step between membrane-less pre-cellular life forms and modern cells that are bounded by ion-tight membranes. Such porous membranes could house various protein and polynucleotide translocases, favouring horizontal gene transfer, gene mixing, and sharing of enzymes and their products between the first life forms, features that are considered essential for the early stages of the evolution of life.

    Maybe that article can make it easier for a layman to understand some important details and facts in your blog article, Rosa? I don't know, but I hope it will do so.

    BTW: A couple of weeks ago I read another interesting article about our cells ("Four billion-year-old chemistry in cells today?"); see: .

    The message goes like this: Some of the chem­i­cal pro­cesses that first gave rise to life may be still at work in liv­ing cells.

    Here's a quote from that article: The new re­search dis­cusses how small pock­ets of a cell con­tin­ue to per­form si­m­i­lar re­ac­tions in our bod­ies. These re­ac­tions in­volve iron, sul­fur and electro-chem­is­try and are still im­por­tant for en­er­gy-getting pro­cesses such as respir­a­t­ion in an­i­mals and pho­to­syn­the­sis in plants.

    “Cells con­fine cer­tain bits of dan­ger­ous chem­is­try to spe­cif­ic com­part­ments of the cel­l,” said lead re­searcher Jan­neke Balk of the at the Uni­vers­ity of East An­glia in the U.K. “For ex­am­ple small pock­ets of a cell called mi­to­chon­dria deal with electrochem­is­try and al­so with tox­ic sul­fur me­tab­o­lism. These are very an­cient re­ac­tions thought to have been im­por­tant for the or­i­gin of life.

    “Our re­search has shown that a tox­ic sul­fur com­pound is be­ing ex­ported by a mi­to­chon­drial trans­port pro­tein to oth­er parts of the cell. We need sul­fur for mak­ing iron-sul­fur cat­a­lysts, again a very an­cient chem­i­cal pro­cess.” A cat­a­lyst is a mol­e­cule that fa­cil­i­tates chem­i­cal re­ac­tions be­tween oth­er mol­e­cules.

    So IF God is the one who created life, why did He chose such complex solutions? I really doubt that God can be an omnipotent, omniscient, omnipresent and omnibenevolent divine entity.

  2. I've always admired the imaginations of Creationists. Don't worry, they're come back with something.

  3. Another interesting fantasy story from the minds of evolutionists.

    When an engineer answers a problem and comes with a solution, he first needs to see if the solution is doable.

    Looking at things from this side, the side where we know life exists, and picking a path supposedly taken that got us here is laughable. This is at best, a historical hypothesis. There is no reason to believe the blind and incredible path described is the one taken. This is what evolution is all about: proposing a historical hypothesis based on assumptions that have not been proven, demonstrated, or even logically shown to be plausible . It is no different than biblical creationism other than being slow.

    Of course, it is not mentioned that known living cells requires tens of thousands of proteins and over five hundred enzymes to sustain life.

    *It is possible for a single hypothetical proto-cell to be the ancestor of all the diversity of life today / Evolution is powerful enough to invent and assemble organs and biological processes, and produce multicellularity from unicellular ancestor.

    On a side note: "A claim made without evidence can be dismissed without evidence", what is the evidence for this claim, lest we dismiss it without evidence.

    1. Dragon fang.

      Sorry you felt you had to open with a condescending ad hominem. Do you ever wish you had something better than an infantile Bronze-Age superstition to use as an excuse to abuse strangers in order to feel better about yourself?

      Have you written to the journal concerned to explain to the editor why he was wrong to publish that paper and to present him with your research findings which refute it?

      Perhaps you could demonstrate you know what you're talking about by explaining why natural selection acting on natural variation would NOT lead to an improved ability to produce descendants.

      You could also try explaining what lies behind your curious assumption that somehow the purpose of evolution was to arrive at where we are today?

      Take your time. When you've managed that, try defining 'life' for the readers and let's see how you do.

    2. Dragon fang.

      By the way, I wrote this especially for people who think they don't believe in evolution. It might help you but you probably would rather have ignorance - So You Think You Don't Believe In Evolution.

  4. It seems that you misunderstood the meaning of ad hominem. If I discredit their or your argument based on irrelevant personal characteristic such as believing in evolution as the origin of the diversity of life, then that would be the case. I simply made a statement that a group of evolutionists came up with a fantasy story and explained my reasoning.

    Your bronze age jab implies that you believe arguments from novelty are valid. This is unrelated since Greek philosophy, which is still in-print, predates the age you mentioned. And the technology of ancient Egyptians, Greeks, and Romans are respectable.

    Whether I send a message to the editor or not is logically irrelevant to the discussion. If it is, then why are you taking The Origin of Species, which was never peer reviewed, seriously?

    You are using a trite and cliche strawman (reflected in the article you recommended) Rosa. My argument is that evolution have not demonstrated any mechanism powerful or intelligent enough to be responsible for all the diversity of life from an original proto-cell ancestor. Please do not redefine the theory of evolution as "genetic inheritance"; nobody is arguing about species fixity.

    Evolution and natural selection are a fact and an ongoing process that generally strengthen species in their environment. I have no argument against that; I never argued that evolution doesn't occur, only that it isn't intelligent or powerful enough. Evolution does contribute to the diversity of life, but observed contributions are simply insignificant until evolutionary mechanisms demonstrate the capability of designing, assembling, and sustaining biological systems. The foundations and assumptions behind the ToE must be shown to not be a fantasy equivalent to slow creationism.

    We can't define life as a substance, but describe what it does as a process. However the point you seem to be making (adaptability being one of the processes) falls under the strawman. Strawmen get burned.

    1. Dragon fang

      >It seems that you misunderstood the meaning of ad hominem<

      No I didn't, but thank you for confirming your ignorance.

      Any more of your infantile abuse and idiotic posturing as an expert in a subject about which you appear to be abysmally ignorant will be removed. This is for normal adult.

      I suggest you read my blog on Dunning-Kruger Syndrome so you can understand why people don't take you seriously and why you've needed to resort to abusing strangers so you feel better about yourself..

  5. @Dragon fang: Here are two other questions I would like you to answer:

    1) Why do all cells have the complete genome (see: )? I'm thinking of your engineer metaphor here above: "When an engineer answers a problem and comes with a solution, he first needs to see if the solution is doable."

    For an omnipotent and omniscient Creator it should, without any doubt, be possible do make all the cells tailor-made, without any "ballast" containing all the genome.

    In the Pharyngula article I linked to PZ Myers says, "My short answer: because excising bits of the genome has a high cost and little benefit, and because essentially all of the key exaptations for multicellularity evolved in single-celled organisms, where modifying the DNA archive would have serious consequences for all the daughter cells."

    Yes, Myers is right. But for God there wouldn't be any such problems, so either God is lazy or a bad "engineer". In short: Why create multicellularity by starting from a single-celled organism, if you are an omnipotent Creator? What can be the reason behind that divine decision?

    2) My second question to you, Dragon fang, is about exaptation; for details see: .

    A quote from that article: Exaptation [...] describe[s] a shift in the function of a trait during evolution. For example, a trait can evolve because it served one particular function, but subsequently it may come to serve another. Exaptations are common in both anatomy and behaviour. Bird feathers are a classic example: initially they may have evolved for temperature regulation, but later were adapted for flight. Interest in exaptation relates to both the process and products of evolution: the process that creates complex traits and the products (functions, anatomical structures, biochemicals, etc.) that may be imperfectly developed.

    My question: Do you think, Dragon fang, that a "recycling" of genes and genetical expressions is the #1 method that a divine "engineer" with omnipotent and omniscient traits or qualities would choose to use when constructing/building/creating new organisms?

  6. It seems that you do understand ad hominem, Rosa.

    As for Helmer's questions:
    The argument from poor design goes something like this:

    1- If God designs, then his design should be optimal.
    2- Certain designs are suboptimal.
    c: God was not responsible for those designs.

    The question is: Optimal for what? We aren't designed to jump over mountains or swim in deep ocean. We aren't designed to live forever. That we cannot really know for sure.

    The argument in this point is flawed since it is an argument from ignorance. That you do not see the wisdom does not prove that there is no wisdom. Rather, it must be demonstrated that the design is unwise, which is not possible since we do not know the purpose for the design.
    So good/bad design arguments don't make a lot sense. This is shown by the fact that there are countless examples of "bad designs" that were shown to be useful.

    The remaining 98% of genome that doesn't code is often called "Junk DNA", however they are important for constructing specific types of proteins. Their current and more accurate name is "Non-coding DNA".

    Although it is amusing that we have claims of so-called vestigial organs and no claim of evolving organs.

    Also, that multicellularity started from single-celled organism is less significant than speculation as no mechanism that demonstrate such a feat is presented.


    As for your second question, it is a historical hypothesis; it lacks scientific evidence of it's possibility, and it does not even propose something probable.

    This is based on oversimplification and leaping over steps. Lets take Ken Miller's mousetrap example. Evolution is proposed to work like lego where you connect five pieces, there are thousands, if not millions, of steps involved over millions of years from start to finish.
    So basically a genuine analogy would be a tiny chunk of the mouse trap platform gets created in a generation (Good luck making use of that), and an other tiny chunk gets created in the next generation (I am sure a comparably tiny invisible tumor created by RM will ensure the survival of the species that got it) so forth until they create a board. Then the pieces assemble themselves over tiny steps and somehow get selected.

    Species are biochemically related; we need water, species need each other to feed, and we live in the same planet. Organs can multiple functions. However, the assumptions in your second question are unjustified.

    1. Dragon fang.

      >The remaining 98% of genome that doesn't code is often called "Junk DNA", however they are important for constructing specific types of proteins. Their current and more accurate name is "Non-coding DNA".<

      I allowed this piece of pompous idiocy through because of what it reveals about you We see your abysmal ignorance exposed for all to see. DNA 'constructs' proteins by coding for them. That's what it does. If it 'constructs' proteins it is an active, coding part of the genome, not junk. You clearly have no idea what you are talking about.

      I would advise you to go away and read up on this stuff but you've obviously settled into posing as an expert from a position of abysmal ignorance and obviously don't mind coming across as a pompous idiot so long as you get attention.

      Having shown that you have nothing to offer worth reading, any more of your infantile gibberish will be removed.

    2. @Dragon fang: Here's an excerpt from your comment: You wrote:

      The argument from poor design goes something like this:

      1- If God designs, then his design should be optimal.
      2- Certain designs are suboptimal.

      The question is: Optimal for what? We aren't designed to jump over mountains or swim in deep ocean. We aren't designed to live forever.

      The argument in this point is flawed since it is an argument from ignorance. That you do not see the wisdom does not prove that there is no wisdom. Rather, it must be demonstrated that the design is unwise, which is not possible since we do not know the purpose for the design. (END OF QUOTE)

      MY COMMENT: My knowledge of the English language is unfortunately if not bad at least not so good. Especially to find words with the right shades of meaning. (That's why I prefer to quote from articles so often.)

      Anyhow, if one argues like you do, Dragon fang, then one must ask what's the point with the so-called Intelligent Design movement. No human being is (according to you) able to understand God's wisdom. Therefore we can't even be sure that signs of intelligent design in fact are intelligent designs. Remember what you wrote: The question is: "Optimal for what?"

      So your standpoint opens up for uncertainty and doubtfulness. What seems (in our humans eyes and brains) to be divine intelligent design may actually be non-divine (or divine) unintelligent design. And vice versa, what seems to be unintelligent design can actually be evidence of divine intelligent design (without our knowing it). And if everything is unknowable for us human beings (with regard to intelligent versus unintelligent design), then not only evolution (or ToE as you prefer to call it) but also the Intelligent Deign movement are equally unprovable.

      To finish my argumentation I want to quote from the Wikipedia article about Intelligent Design (see: ), since there I find some important arguments to support my own point of view (instead of yours):

      QUOTE #1:Intelligent design (ID) is the pseudoscientific view that "certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."

      QUOTE #2: Educators, philosophers, and the scientific community have demonstrated that ID is a religious argument, a form of creationism which lacks empirical support and offers no tenable hypotheses.

      QUOTE #3: Proponents argue that it is "an evidence-based scientific theory about life's origins" that challenges the methodological naturalism inherent in modern science, while conceding that they have yet to produce a scientific theory.

      QUOTE #4: ID presents negative arguments against evolutionary explanations, and its positive argument is an analogy between natural systems and human artifacts, a version of the theological argument from design for the existence of God.

      QUOTE #5: Both irreducible complexity and specified complexity present detailed negative assertions that certain features (biological and informational, respectively) are too complex to be the result of natural processes. Proponents then conclude by analogy that these features are evidence of design.

      QUOTE #6: Detailed scientific examination has rebutted the claims that evolutionary explanations are inadequate, and this premise of intelligent design —that evidence against evolution constitutes evidence for design — has been criticized as a false dichotomy.

      To be continued in the next comment.

    3. PART 2 of my long comment:

      Especially quotes number 4, 5 and 6 I want to adduce as an example of your misunderstanding of what science is/means. In science different hypotheses are competing with each other. The hypothesis with the highest explanation power plus the best validation is proclaimed the "winner" (at least until new data and facts appear that undermine that special hypothesis). See also quote #3: Proponents [...] [of ID are] conceding that they have yet to produce a scientific theory.

      What you devote most of your time to (in your comments), Dragon fang, seems to be to attack the ToE and its evidence and conclusions, thereby pretending, presuming and taking for granted that creationism must be the best explanation. Cf. quote #6 here above. It's a false dichotomy to say that "evidence against evolution constitutes evidence for design".

      Furthermore, your argumentation seems to be almost wholly philosophical, i.e. you don't present a single argument built on facts that can be interpreted in just one way (for or against ToE; for or against creationism).

      What you and other creationists take an interest in can be described as cherry picking; see: .

      A quote from that article: Cherry picking, suppressing evidence, or the fallacy of incomplete evidence is the act of pointing to individual cases or data that seem to confirm a particular position, while ignoring a significant portion of related cases or data that may contradict that position. It is a kind of fallacy of selective attention, the most common example of which is the confirmation bias. Cherry picking may be committed intentionally or unintentionally. This fallacy is a major problem in public debate.

  7. Today I read this interesting article about how life might have been "created" without God's helping hand: .

    Some quotes from that article: QUOTE #1) One of the challenges is to create the information strings that can be inherited by cell offspring, including protocells. Such information strings are like modern DNA or RNA strings, and they are needed to control cell metabolism and provide the cell with instructions about how to divide.

    QUOTE #2) “In our computer simulation – our virtual molecular laboratory – information strings began to replicate quickly and efficiently as expected. [...] According to Steen Rasmussen, a so-called self-organizing autocatalytic network was created in the virtual pot, into which he and his colleagues poured the ingredients for information strings.

    An autocatalytic network is a network of molecules, which catalyze each other’s production. Each molecule can be formed by at least one chemical reaction in the network, and each reaction can be catalyzed by at least one other molecule in the network. This process will create a network that exhibits a primitive form of metabolism and an information system that replicates itself from generation to generation.

    “An autocatalytic network works like a community; each molecule is a citizen who interacts with other citizens and together they help create a society”, explains Steen Rasmussen.

    QUOTE #3) “We might have discovered a process similar to the processes that initially sparked the first life. We of course don’t know if life actually was created this way – but it could have been one of the steps. Perhaps a similar process created sufficiently high concentrations of longer information strings when the first protocell was created”, explains Steen Rasmussen.


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