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Evolution Basics: At the Frontiers of Evolution, Part 2: Abiogenesis and the Question of Naturalism

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July 10, 2014 Tags: Creation & Origins, History of Life, Science & Worldviews

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Evolution Basics: At the Frontiers of Evolution, Part 2: Abiogenesis and the Question of Naturalism

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we tackle the question of naturalism before introducing the idea of an “RNA world” that predates modern DNA-based biology.

Weizsäcker’s book The World View of Physics is still keeping me very busy. It has again brought home to me quite clearly how wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat. We are to find God in what we know, not in what we don’t know; God wants us to realize his presence, not in unsolved problems but in those that are solved.

Dietrich Bonhoeffer, Letters and Papers from Prison

In the last post in this series, we left behind the comfortable confines of evolution as a theory (in the scientific sense) and headed out into one of its “frontier” areas – abiogenesis, the hypothesized transition from chemical “non-life” to life. For an American audience, “frontier” immediately calls to mind images of the Wild West – where law and order did not (yet) hold sway, outlaws and renegades were behind every barrel, and justice was dealt from the sheriff’s six-shooter (well, at least that’s how I remember the Hollywood version I saw on television as a child). In short, the frontier was a rough-and-tumble land of conflict and courage a world away from the law and order of the city – and their respective inhabitants had personalities to match.

For abiogenesis, the frontier analogy is surprisingly appropriate. When I read the scientific literature on the topic, I am instantly struck with how, well, speculative it is. This is not the scientific equivalent of quaint New England streets – this is a rough map with large swaths of uncharted territory with perhaps a few wagon tracks through it, at best. Multiple, competing hypotheses abound – was the first life a self-replicating RNA enzyme? Did life start as a metabolic pathway that only later added a heritable molecule of some sort? Did life start near deep sea vents? Did life (or some precursors to life) start somewhere else (as in not even on this planet)? All of these ideas have at least some traction in the scientific literature, and not one of them holds a majority position. It’s the scientific equivalent of the Wild West, complete with interesting personalities “dueling” each other in the scientific literature. The truth of the matter is that we just don’t know.

Let me say that again: when it comes to abiogenesis, we have almost no clue how it might have occurred.

Of course it is at this juncture, as we discussed in the last post, that a great many Christians seize on this professed ignorance to proclaim the failure of evolution as a whole. I too once did so as well, when I held antievolutionary views, so I know full well this temptation. I now realize that this makes about as much sense as claiming the map of New England to be a hopeless mess because Oregon has not yet been fully charted. Unknowns are expected at the frontier – that’s why you go there.

But… God?

But Dennis, you might say, aren’t you assuming that life had a “natural” origin? Aren’t you discounting the possibility that God might have brought life about through supernatural means? Haven’t you capitulated to “naturalism” from the outset?

There is of course much to discuss here, and the topic goes well beyond the scope of this article (or even this series as a whole). Still, the question is a valid one that merits at least a brief reply. Since abiogenesis is a frontier area of science, in principle it could have either what Christians would call a “supernatural” or a “natural” explanation – we simply do not know. Of course, any explanation in science might actually have a “supernatural” explanation, but merely appear to us as the regular outworking of “natural” law. Most Christians avoid such arguments, of course, if the science is well settled – not many of us hold out for a supernatural explanation of weather patterns or human reproduction, for example – choosing rather to see these “natural” events as part of the providence of God. No, it is typically only where less is known scientifically that Christians tend to favor supernatural explanations.

Personally, I am reluctant to ascribe to miracle what is not yet well studied scientifically, since more work may reveal a “natural” explanation – “natural”, of course, meaning part of the reproducible structure of the cosmos that God has put in place and continues to uphold that allows us to investigate it using science. In this sense, “natural laws” can be seen as part of God’s covenant faithfulness to His creation, something that my colleague Arnold Sikkema has written on (PDF) and I have found helpful. So, whether the origin of life was “natural” or “supernatural” it was of God, and there is nothing to be lost by attempting to investigate it through the scientific method. Perhaps another way to put it is that, as a scientist, I am curious just how far this regular, reproducible structure of the cosmos extends – does it extend all the way to a transition between non-life and life? Did God, in His wisdom, fashion the cosmos in such a way that chemicals could become alive? Just how deep does the rabbit hole go? While I suspect that life had a “natural” origin in the sense above, I recognize that not all Christians feel the same way. The reason for this hunch – and it is a hunch – is that I see pointers in what we do know that suggest it to be the case.

Hints & whispers

One such “pointer” to a possible chemical past for life on earth is a feature of all living things at the very heart of what it means to be alive in a molecular sense. One of the first things one learns as a biologist is that macromolecules have divided the labor between heredity and enzymatic function: DNA is for genes, and proteins are for catalyzing reactions. Then, one learns about the various forms of RNA – a class of molecules that, interestingly, in some cases have both hereditary and enzymatic function simultaneously. Then one learns that the key enzyme at the center of the cellular machinery is in fact not a protein enzyme, as one would expect, but rather an RNA molecule – the ribosome. Ribosomes are responsible for using RNA templates to direct protein synthesis, and proteins go on to complete the loop by copying the cell’s DNA, which encodes the information for making RNA. In a significant sense, it’s all about RNA: RNA enzymes using RNA templates to make proteins that copy the cell’s DNA (which contains the crucial RNA information in a more stable form). When the chemical structure of the ribosome was determined in the early 2000s it was demonstrated that the few proteins associated with it are not part of its enzymatic function – which was a significant surprise for many molecular biologists at the time. To many of them, this absolutely crucial RNA enzyme using RNA templates at the center of cellular life was suggestive – suggestive that life once passed through a stage where RNA was the major player in heredity and enzymatic function, rather than the DNA/protein world of the present.

In the next post in this series, we’ll explore this proposed “RNA world” – a hypothesis that has gained some experimental support in recent years.

For further reading


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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Gregory - #85962

July 10th 2014

“when I held antievolutionary views”

Do you now hold anti-evolutionism views?

Oregon map: https://www.google.com/maps/place/Oregon/@44.1419049,-120.5380992,7z/data=!3m1!4b1!4m2!3m1!1s0x54936e7c9b9f6a55:0x7d4c65db7a0bb876

p.s. scientific methodS - plural


sy - #85963

July 11th 2014

Dennis

I like your analogy to the Wild West quite a lot. I also like your comments about both natural and supernatural causes coming from God. In the case of abiogenesis, there are some real questions about how modern life arose (as opposed to proto life, which I believe includes RNA world). For example, even if there was a phase in which RNA was acting as the chief heredity information molecule, and an important catalyst, how did that system “evolve” (in the absence of Darwinian mechanisms of evolution) into a DNA based genetic coding system that gets translated into phenotype. 

I dont see a viable “natural” way that such a transition could occur. On the other hand, I cant imagine a “supernatural” mechanism either. If LUCA came into life by an act of God, exactly what kind of act could it have been?

I suppose I am jumping the gun here a bit, and that you will get to these issues later. I am looking forward to it. 


g kc - #85965

July 13th 2014

Dennis,

I’ve been browsing Biologos for some time now, and today felt compelled to comment.

You wrote (with MY EMPHASES) “When I read the scientific literature on [abiogenesis], I am instantly struck with HOW, well, SPECULATIVE IT IS… MULTIPLE, COMPETING HYPOTHESES ABOUND… All of these ideas have at least SOME traction in the scientific literature, and NOT ONE of them holds a MAJORITY position. It’s the scientific equivalent of the Wild West, complete with interesting personalities “dueling” each other in the scientific literature. The truth of the matter is that WE JUST DON’T KNOW.”

I think your characterization of the abiogenesis literature could be said also of the evolution literature in general. Certainly some would argue over the perceived levels of speculation in the two, but that would be only a disagreement over perceived degree.

Related to this, your noting of an absence of a “majority position” leads me to believe you think having a majority position (i.e. “consensus”) makes the position NOT speculative, or at least less speculative. I think we both know that the truth that real science is supposed to be after can be completely unrelated to any current consensus. That is, scientific truth is not determined by consensus or majority positions; it’s determined through the scientific method involving observation and testing and confirming hypotheses.

Evolution is quite like abiogenesis in that it has never been observed in nature, has never been orchestrated in a lab, and has multiple competing hypotheses as to how it happened.

And when I say “how”, I mean in detail. For just one of limitless examples, you mentioned “human reproduction” in this piece. How did sexual reproduction evolve and why? Asexual repro seems much easier and more efficient, evolutionarily-speaking, doesn’t it? How do you GRADUALLY go from an asexual system to a sexual system? What do the many intermediate stages look like and how does the organism reproduce during the “construction phases”. How was reproduction happening for the millions/billions of years prior to the (undoubtedly) simultaneous “completion” of both male and female reproductive systems?

I see that your evolution “basics” series is up to 42 articles, not including the two on abiogenesis. (Makes me wonder how many articles an “advanced” series would entail.) Perhaps you can expand the “basics” series further with pieces on the evolution of sexual reproduction, since reproduction is crucial to evolution, and in fact to all life.

So, I see the literature on evolution to be essentially as speculative as that of abiogenesis. I think a big reason why over 40% of those polled by Gallup dismiss any form of evolution leading to human beings is that they find the so-called science speculative, NOT “settled”. They don’t have a war on science, they have a war on speculation as “science”. You would NOT find over 40% of potential jurists dismissing the science of DNA forensic evidence. 


sy - #85971

July 15th 2014

g kc

I dont agree that evolution and abiogenesis have much in common when it comes to speculation and uncertainty. The evidence for evolution in general, and in all specific cases, is quite firm, and more importantly all leads to a single unified concept, namely genetic variation followed by natural selection. There are, as you suggest many issues concerning some of the details, for example, are all mutations leading to genetic variation random (as the new Darwinian paradigm states) or not (as I believe, based on a body of often ignored literature on bacteria). But the basic framework of Darwinian evolution has so much explanatory power, that it has indeed allowed almost all biologists to agree that it is the truth about how species came to be.

Examples of major leaps in evolutionary history, such as sexuality, multicellularity, new body plans, and so on, do require (in my view) more than the standard slow, progressive point mutation model, but that is not to deny the underlying premise that natural selection (as we know it, using a DNA based code, and a large set of versatile proteins) is extremely powerful at making enormous, and even rapid at times, changes in the structures and functions of organisms.

And this is where I see abiogenesis as being a totally different thing. (Darwin and Dawkins agree, btw). The current evolutionary machinery involving error free translation of a genotype into phenotype which is then the target of selection, did not exist before modern DNA based life. So in that case, your question is valid. If it couldnt arise by natural selection, how did it?


g kc - #85974

July 15th 2014

Sy,

With MY EMPHASES:

“The evidence for evolution in general, and in ALL SPECIFIC CASES, is quite firm…”

Yet you admit, as you must, that many, many things (e.g. “sexuality, multicellularity, new body plans, and so on”) are beyond the explanatory power of current evolution theories.

 

“But the basic framework of Darwinian evolution has so much explanatory power, that it has indeed allowed ALMOST ALL biologists to agree that it is the truth about how species came to be.”

See again my comments to Dennis regarding the essential irrelevance of “consensus”.

 

“… natural selection (as we KNOW it, using a DNA based code, and a large set of versatile proteins) is extremely powerful at making ENORMOUS, and even RAPID at times, CHANGES IN the STRUCTURES and FUNCTIONS of organisms.”

We both know you can’t give an example of such enormity and rapidity in producing a complex system such as sexual reproduction. How about something simpler, such as an organ. How about the evolution of the eye? If not the eye, what would be your top example supporting your quote?

 

“And this is where I see abiogenesis as being a totally different thing. (Darwin and Dawkins agree, btw).”

I think Darwin and Dawkins are short-changing their imaginations. Evolutionists propose evolution, because all living things have DNA and thus “must” have a common ancestor. Likewise, they could propose abiogenesis, because all living things have chemicals in their bodies and thus the common ancestor sprung from a coalescing of chemicals. It’s pretty easy. It’s not so totally different at all. But one advantageous difference (for science) is that abiogenesis would be instantaneous, by definition. You wouldn’t have to wait millions or billions of years to see it, like with the unfortunate case of evolution. It’s just too bad no one’s ever witnessed abiogenesis. 


bren - #85977

July 15th 2014

Hi g kc, I’d like to butt in if I may,
As to the idea of a scientific consensus, I wonder if there isn’t a great deal of confusion about this very point.  It is true that truth is not decided by vote (or anyway, I would certainly vote to support this statement), but I’m afraid that in the eyes of education legislators, politicians and the general public, the scientific method is simply not available to check every textbook fact, so their only access to the most reliable conclusions in a complex field is by way of reference to the majority opinion of those who are considered to be in the best position to know.  Extensive knowledge (nearly all knowledge) is impossible where this approach is not followed.  And why would you suspect that those same experts who make up this consensus have not used the very scientific method that you suggested to arrive at this agreement in the first place?  They aren’t just sitting at home cooking up atheistic plots to suppress theist-friendly lines of
investigation, they are applying the critical methods and we are the beneficiaries of the hard work that you seem ready to dismiss.  Science isn’t just the scientific method (if that was the sum of it, it couldn’t ever have any results by definition), it is also the body of knowledge that can be considered as the fruits of this method, and frankly, this comes down to the consensus of the scientific community.  I can’t imagine what you or anyone else would suggest as a replacement for this.
With regard to “sexuality, multicellularity, new body plans, and so on”, there is nothing to give us the impression that these developments are contrary or damaging to evolutionary theory, so it is difficult to see why they would be raised as objections to the consensus.  It would help if you could clarify what you had in mind.
Re:  “Evolutionists propose evolution, because all living things have DNA and thus “must” have a common ancestor.”
I’m sorry but you are completely pulling this out of your hat and you should be called on it.  No historian of science could possibly endorse such a flippant remark.  Darwin advanced the mere possibility of a common ancestor based on telling homologies etc and knew nothing about DNA.  The common denominator of DNA and the genetic patterns between species have since combined to make the unity and common ancestry of life unavoidable.  Evolution was proposed for completely different reasons and the idea of a universal common ancestor was merely a vague possibility for a long time.  Can I ask what gave the impression that this was a fair or accurate statement?


g kc - #85979

July 15th 2014

Bren,

“Science isn’t just the scientific method (if that was the sum of it, it couldn’t ever have any results by definition)…”

In other words, having false or highly questionable results is better than having no results. At least you’ll have something to publish.

“… [science] is also the body of knowledge that can be considered as the fruits of this [scientific] method, and frankly, this comes down to the consensus of the scientific community.”

In other words, the “fruits” of science (evolution “science” in particular) is largely “consensus”, certainly not proofs. Not even observations, and interpretations thereof, universally and repeatedly and independently made, or results of hypothesis testing universally and repeatedly and independently confirmed.

Instead, we get “scientific” articles on abiogenesis, multiverses, eyes evolving from sensitive skin, and limitless “what-ifs” in the journals “Nature” or “PNAS” or countless others.

Instead we get this (Note: Biologos founder Francis Collins gets a mention.):

http://online.wsj.com/articles/hank-campbell-the-corruption-of-peer-review-is-harming-scientific-credibility-1405290747

More on peer-review perversities:

http://theconversation.com/hate-the-peer-review-process-einstein-did-too-27405

 

“I can’t imagine what you or anyone else would suggest as a replacement for this.”

How about NOT publishing or publicizing something as a “fact” (or even as a certainty beyond any reasonable doubt) unless you’ve got proof (or evidence towards a proof beyond any reasonable doubt)? Think that’s too harsh? Too much of a threat to job security and prestige for academics (PARTICULARLY in the fields of biological AND cosmological evolution)? And all those prestigious, peer-reviewed journals might dry up. That would indeed be rough, particularly in this economy. But would it be more right?

 

“With regard to “sexuality, multicellularity, new body plans, and so on”, there is nothing to give us the impression that these developments are contrary or damaging to evolutionary theory, so it is difficult to see why they would be raised “as objections to the consensus.  It would help if you could clarify what you had in mind.”

My mistake. I forgot the ready scientific answer: “They evolved”, a.k.a. evolution of the gaps.

 

“Re:  “Evolutionists propose evolution, because all living things have DNA and thus “must” have a common ancestor.”I’m sorry but you are completely pulling this out of your hat and you should be called on it.  No historian of science could possibly endorse such a flippant remark.”

My statement was purposefully short and simple, but how was it not fair or accurate? On this very site I’d BET you could find multiple articles defending evolution and common ancestry on the basis of DNA analysis showing x% DNA commonality between this and that (usually man and chimps) and entire proposed phylogenetic “trees of life”. That’s what would give me the impression that mine was a fair and accurate statement. Do you think I’d win my bet?


bren - #85988

July 16th 2014

G kc:  ““Science isn’t just the scientific method (if that was the sum of it, it couldn’t ever have any results by definition)…”
In other words, having false or highly questionable results is better than having no results. At least you’ll have something to publish.”

Bren: “In other words” usually means that you are about to paraphrase what was just said.  I look at these two sentences and I can’t fathom how the second is meant to paraphrase the first.  I was pointing out that science is usually regarded as the scientific method (rather a loose alliance of rigorous methods for testing hypotheses) as well as the body of knowledge gathered using the scientific method.  You then go on to paraphrase this as my saying that false and highly questionable results are completely acceptable so long as we get to publish.  WHAT?!!  If that is how you are going to treat every statement I make, we might as well not be speaking a common language.  Do I need to go on through the entire post if you are going to be that cavalier about the very first sentence you handle?  You literally tried to make it mean nearly the opposite of what it does mean by the simplest rules of grammar.  Were you under the impression this wouldn’t be
noticed or did you just fail to read the sentence before you copied and pasted it?  I will assume it was just carelessness since no one is dishonest about such things when taking the trouble to copy-paste the refutation in the same breath.

I’ll go on anyway, in spite of the fact that I apparently can’t be confident that you won’t trample all over the normal everyday meaning of my words in your response, please avoid this if you don’t mind.  You then go on to demand “proofs” as though we were dealing with a mathematical theorem (this is unfortunately a small clue that you may not be as familiar with the sciences as I was hoping, which is fine, but it makes it a little surprising that you should pretend to be such an insider that you are able to ferret out an atheistic money-grubbing conspiracy amongst scientists).  For some reason, you don’t seem to think that the scientists who are at the base of the modern consensus have bothered to be the least bit rigorous.  You use words like “observations, and interpretations thereof, universally and repeatedly and independently made” as though these ideas would come as nasty shock to so-called “working” biologists who are
apparently only interested in getting their next paycheck and cashing in on the big lie.  This claim just doesn’t intersect with reality.  Seriously, just borrow a recent edition of “Evolution” (Wiley) at the library and see if you can identify either an ongoing controversy about the validity of evolution or a lack of rigor in the methods being used, maybe you can look at editorials and find snide insider insinuations about how they are riding the evolution money wave.  This is just a fantasy world; you may not agree with their findings, but the methods are careful and rigorous, the controversies are heated and technical and the findings are neither overstated or unsupported.  One needs to be entirely detached from the scientific community to do anything other than laugh at such conspiracy theories but they seem to be common currency in creationist circles.  I’m quite serious about borrowing a journal copy; it might lead you to suspect that
you’ve been duped about what’s really going on in the sciences.  You can lump your “fears about job security and loss of prestige” into this last paragraph; you simply don’t seem to know what real biologists are up to and have invented a bracing fictional account to fill in the blank.  Sorry to be a bit sharp, but is an insult to hard-working biologists when you invent such bunk and then throw it at them in the form of accusations.  Do you know how much work, care and sacrifice you are dismissing from your comfy armchair?  It seems not.

I agree with you that there are “what-ifs”, as you put it, when discussing individual evolutionary pathways and the selection pressures that may have contributed, but these are usually stated as hypotheses and in nearly all cases, scientists have no illusions where there is no available (or possible) evidence and they don’t exactly hide the difference between a conjecture and an established theory.  Popular science books aren’t always so sober and are not reviewed in the same way, so obviously check your sources before claiming carelessness or fraud on the part of scientists.  Is a book written by a journalist all excited about a connection between Zen Buddhism and quantum theory?  Don’t blame Niels Bohr. That said, your being incredulous about something is a very poor substitute for an actual argument.

G kc; “My statement was purposefully short and simple, but how was it not fair or accurate? On this very site I’d BET you could find multiple articles defending evolution and common ancestry on the basis of DNA analysis showing x% DNA commonality between this and that (usually man and chimps) and entire proposed phylogenetic “trees of life”. That’s what would give me the impression that mine was a fair and accurate statement. Do you think I’d win my bet?”

Bren:  I’ll try this again in a bit more depth, since it seems you didn’t read the rest of my paragraph (or at least you ignored it).  You stated clearly that the reason that evolutionists propose evolution is because all living things have DNA (and therefore must have had a common ancestor).  This is an accurate paraphrase.  This also makes no sense.  Darwin “proposed” and supported evolution long before anything about DNA was known let alone that all animals (and many viruses) have DNA.  Heredity was something of a mystery to Darwin and his contemporaries, though he had a basic idea of the patterns of variation and conservation of traits. You are putting the cart way before the horse, since the modern synthesis comes well before Watson and Crick.  The fact that we all have DNA and that we also largely have the very same translation system is certainly a good modern corroboration of the idea of common ancestry, since no other idea seems to explain why
the DNA to protein translation system should be conserved across the board, but this is not even close to being the reason that evolutionists propose evolution (or ever have); you simply can’t get one from the other.  This idea of yours would be news to historians, so please support it with something other than impossible timelines.  Perhaps you happen to know an evolutionist who thinks the whole thing is based on the fact that we all have DNA?  Strange, but possible.  For the idea that x% DNA commonality between this and that species indicates common ancestry; no one seems to make that claim on this site for obvious reasons so please give me a reference or recheck the blog that you are referring to (I think you will find that you misunderstood).

I’m not especially interested in defending the integrity of scientists as a life goal, but I don’t particularly feel like standing by while wild accusations of dishonesty, bribery and cowardice are thrown at all evolutionary biologists by someone who doesn’t give the slightest impression that he’s ever met one or read any of their papers.


bren - #85989

July 16th 2014

Correction to the above: “all animals (and many viruses) have DNA” is true but a bit silly, I guess I meant all cellular life if you don’t include special cases red blood cells…


g kc - #85992

July 16th 2014

Bren,

I stand by the first point (which included some hyperbole).

I took “results” to mean something that really MEANS something scientifically. More specifically, “results” should be proofs or verifications or repudiations, or even surprising discoveries (which would in turn be subject to testing and verification) coming from the proper exercise of “the scientific method”. Anything other than this is speculation as far as I’m concerned. (And speculations are often false or highly questionable.)

What did YOU mean by “results”?

 

“…you simply don’t seem to know what real biologists are up to and have invented a bracing fictional account to fill in the blank.”

I have the utmost respect for real biologists. I just don’t think much of “evolutionary” biologists.

 

“… I agree with you that there are “what-ifs”, as you put it, when discussing individual evolutionary pathways and the selection pressures that may have contributed, but these are usually stated as hypotheses and in nearly all cases, scientists have no illusions…”

But would you agree that in most, if not all cases, the “what-ifs” NEVER include the POSSIBILITY that there was NO evolutionary pathway (i.e. that evolution didn’t happen)?

 

“For the idea that x% DNA commonality between this and that species indicates common ancestry; no one seems to make that claim on this site for obvious reasons so please give me a reference or recheck the blog that you are referring to (I think you will find that you misunderstood).”

Perhaps you’re right, and perhaps I’d lose my bet.

If I find enough time, I might try to find an example of an author here who DOES make that claim. In the meantime, I decided to try a quick search and typed “common ancestry” into the BioLogos search slot. The top results were a series of articles by Dennis Venema titled “Intelligent Design and Common Ancestry”. In Part 2 of the series, the first paragraph reads:

“In the last post in this series, we examined Casey Luskin’s attempt to minimize the level of identity that the human and chimpanzee genomes share. Luskin, with his concern to discredit the evidence that humans and chimpanzees share a common ancestor, suggested that the genuine identity value for these two genomes might be as low as 70%. Accordingly, we took the time to explain why his approach was misguided, and in the process learned about how genomes are sequenced and compared. As we saw, the human and chimpanzee genomes are in fact highly identical to each other, with identity values at 95% or more, depending on how the comparison is done. Such values are obviously highly consistent with shared ancestry, which would have humans and chimpanzees arriving at our differences by subtle modifications of our ancestral, shared genome.”

Gosh, maybe my search won’t take so long after all.


bren - #85997

July 17th 2014

I’ll start by your last point first; I’m amused at how easily you wandered into that mistake, in spite of my having pointed it out in advance.  The blog from which you quoted was exactly the one I was thinking of yet you haven’t even bothered to check whether it supports your phrase.  I’ll repeat your phrase for convenience: “I’d BET you could find multiple articles defending evolution and common ancestry on the basis of DNA analysis showing x% DNA commonality between this and that (usually man and chimps)”
I don’t know if you are simply not a very careful reader or how I should otherwise explain it; Venema, in the blog in question and in the quote provided, does not in any way support evolution and common ancestry based on this percentage.  In fact, if you actually read the blog, he repudiates any such idea (since the creationist who he is responding to, Casey Luskin, apparently thinks that the percentage is important for the idea of common descent and Venema is clear that he totally disagrees).  Venema regards Luskin’s efforts to push down the percentage as scientifically suspect and treats it as such as a part of his overall review of Luskin’s work, but does not agree with Luskin that it has anything to do with the question of common descent.  If you are suspicious of what I just said, please re-read the blog.  To be fair, maybe you didn’t read the blog at all (not wise when you are using it to support your point), maybe you just read the above summary of the blog, where the point is ambiguous.  If this is the case, I’m sorry for assuming and I think you can easily correct your mistake by going back to the previous post in his series.

Anyway, I actually have no idea what point you were originally trying to make with this incorrect phrase.  I was criticizing your sentence to the effect that evolution is only proposed because all things have DNA.  This is completely false and I don’t even know any creationists who would agree with such an idea.  To not bother to defend the point I had criticized and then to run off with mistaken rants about how biologos uses the % commonality between chimps and humans to support common ancestry (which they don’t) is strangely off topic and I can’t understand how it is supposed to connect to your original statement.

The in-between points don’t strike me as being substantial as they are based on your opinions and I see no reason to think you have enough background knowledge to meaningfully offer such opinions; the fact that you don’t think much of evolutionary biologists is pretty darn weak considering that you don’t know any, you haven’t apparently read any of their scientific work, and all you seem to know about them is filtered to you by popular literature and by an antagonistic subculture.  If you aren’t willing to pay due diligence to intellectual honesty in studying the sources and considering the history and methods, you renounce all rights to an informed opinion, so I’ll take what remains for what it’s worth.

Now onto your first point.  I carefully lined up two sentences up for you (though you seem to have cut out some of the context from my initial sentence), and then pointed out that yours cannot be a paraphrase of mine.  Even taking into account hyperbole, they have completely different meanings (hyperbole would exaggerate, not contradict the meaning of the first sentence).  Your response is to quibble about the meaning of the word “results”.  Yes, G kc, we both have in mind something like the same meaning and no, this doesn’t have anything to do with the fact that you massacred my sentence and completely changed its meaning when paraphrasing it.  Yes this is a minor point, but the truth is, it is symptomatic of a dishonest (I originally thought you just
misunderstood, but at this point..) approach.  If you can take and twist any phrase that is said beyond recognition in your own mind or in your response, then let it be no surprise that you can come to any conclusion you want to without facing opposing inconveniences.
I would have taken you more seriously if you had said “I don’t think these results actually come from the scientific method”; it would mean that you took my sentence at face value and then disagreed with my point of view.  I would oppose this, but at least we would be having an honest debate.  Instead, you decided to go with; “here’s what you really meant” and then completely changed the sentence.  Please have the good grace to let me decide that what I said was what I really meant and the honesty to admit when you have misrepresented my views.


g kc - #86007

July 17th 2014

Bren,

I’ll break this response into three couple parts.

Part 1:

Regarding my first point, which has caused you so much irritation, let’s start over and replay your words in greater context, or at least with more of your words before and after the ones I had previously quoted:

“They aren’t just sitting at home cooking up atheistic plots to suppress theist-friendly lines ofinvestigation, they are applying the critical methods and we are the beneficiaries of the hard work that you seem ready to dismiss.  Science isn’t just the scientific method (if that was the sum of it, it couldn’t ever have any results by definition), it is also the body of knowledge that can be considered as the fruits of this method, and frankly, this comes down to the consensus of the scientific community.”

Perhaps I just take words too seriously, pay too much attention to them. Because now I’m thinking that a reasonable understanding of the above words could be even more shocking to you than what I’ve already said. Re-read your words above. Using common grammar, common understanding and common sense, I would say the words by themselves indicate that

1)      the author is saying that neither science nor the scientific method has any “results”.

2)      the author is saying that science produces “fruits” such as “a body of knowledge” and “consensus”, but neither of these are “results”.

I stand by everything I said on this matter. Both evolutionist and non-evolutionist can and would agree on empirical findings, on repeated and confirmed observations. They would agree on “results”. These are not speculative. These are beyond dispute. However, they would not necessarily agree on the interpretations of those “results”. And it seems you’re trying to protect and promote just one side’s interpretations.  

 

Part 2:

You accuse me of a “dishonest approach”. And you, as with many if not all evolutionists, make presumptions of “fact” which are, in fact, false.

You wrote “the fact that you don’t think much of evolutionary biologists is pretty darn weak considering that you don’t know any, you haven’t apparently read any of their scientific work, and all you seem to know about them is filtered to you by popular literature and by an antagonistic subculture.”

False. Although I suppose I won’t be able to prove it to you (proving something can be hard!), I can tell you that I’ve “known” at least one evolutionary biologist – David Sloan Wilson, Distinguished Professor of Biology and Anthropology and head of the Evolutionary Studies program at Binghamton University. About 6 or 7 years ago, I had a 2-hour one-on-one with him. He had invited me for a talk over beers after he had read my letter-to-the-editor in the newspaper which had printed an opinion piece of his. (My letter, and later emails, were not what he’d consider a favorable review.) His opinion piece was making the case that evolution could be used to improve urban planning. I’m not kidding. The meeting was quite remarkable. I can’t remember everything we discussed, but two things still stand out in my memory:

1)  In response to my arguments against evolution and its “evidences”, his repeated descriptions of lizards (desert lizards, as I recall) whose coloration provides them a survival advantage. 

2)  His explanation of how he chose his occupation. He wanted to get out from under the shadow of his famous father (author Sloan Wilson (“The Man in the Grey Flannel Suit”)), do something completely different, liked science and particularly biology, and (this is the really memorable part) “so, of course, I became an evolutionary biologist.” As if “biologist” and “evolutionary biologist” are synonymous. Unforgettable.

You’re also mistaken in your presumption that I haven’t read “any of their scientific work.” I’ve read many of them. But I’ve found that, for the most part, ‘If you’ve read one you’ve read them all.’ Countless “what-ifs”, “coulds”, “may haves”, “possiblys”, etc.

 

Part 3:

As to my plan to find support for my simplified claims (“Evolutionists propose evolution, because all living things have DNA and thus “must” have a common ancestor”; “defending evolution and common ancestry on the basis of DNA analysis showing x% DNA commonality between this and that”), I may need more time. But as I did yesterday, today I did a quick search, but this time outside of BioLogos. It’s not exactly what I may be looking for, but maybe I’m getting warmer:

 

“Was it not already obvious, from the discovery and deciphering of DNA, that all life forms are descended from a single common organism—or at least a basal species? No, says Douglas Theobald, an assistant professor of biochemistry of Brandeis University and author of the new study, detailed in the May 13 issue of Nature. (Scientific American is part of Nature Publishing Group.) In fact, he says, “When I went into it, I really didn’t know what the answer would be.” 

“… By plugging these sequences into various relational and evolutionary models, he found that a universal common ancestor is at least 10^2,860 more likely to have produced the modern-day protein sequence variances than even the next most probable scenario (involving multiple separate ancestors).

“… The mid-20th-century discoveries about the universality of DNA “really nailed it for people” in terms of establishing in popular—and academic—culture that there was a single universal common ancestor for all known life on Earth, Theobald says. And since then, “it’s been widely assumed as true,” he notes. 

“But in the past couple decades, new doubt has emerged in some circles.

“With advances in genetic analysis and statistical power, however, Theobald saw a way to create a more comprehensive test for all life

“He ran various statistical evolutionary models, including ones that took horizontal gene transfer into consideration and others that did not. And the models that accounted for horizontal gene transfer ended up providing the most statistical support for a universal common ancestor… Theobald says his most surprising results were “how strongly they support common ancestry.”

http://www.scientificamerican.com/article/universal-common-ancestor/

As I said, perhaps not exactly what I’m looking for. But I may never find what I’m looking for, because the evolution positions keep “evolving”. As the article’s last paragraph says:

“On a more foundational level, Penny says, the paper should not put an end to the assessment of ancestral assumptions. Instead it should be a reminder that “we have never thought of all possible hypotheses,” he says. “So we should never stop considering some new approach we haven’t thought of yet.”

I guess some people would say they have “results”.

 

P.S.

I don’t think I want to continue this correspondence, Bren. I’d rather not engage with people who accuse me of “dishonest” tactics and who state “facts” about me which I and God know are false. (Reference Part 2 above). I’m not surprised by it. I’d just rather not put up with it. 


bren - #86022

July 21st 2014

Gkc,

Point 1:

Neither of your interpretations are even a plausible paraphrase of what I said.  Of course I’m saying science has “results”.  Of course I’m considering “fruits” such as “a body of knowledge” and “consensus”, to be the “results” of the rather wide-ranging activity called science (these being obtained by application of the scientific method, debate, criticism, etc). I’m saying precisely the opposite of what you are asserting.  Just read your sentences and mine side to side and see if you can pull out the same meaning.  It’s weird, since you otherwise seem to write excellent English, so I can’t imagine what is causing you to persist in reinventing what I said, even when it has no linguistic or logical basis, somehow thinking that quoting what I said in greater length vindicates you.  I was earlier flip-flopping between suspecting intentional insincerity (though I can’t work out what could possibly motivate this) and careless
misreading (though I can’t work out what could cause this so repeatedly).  It’s not even clear how I could refute your paraphrase, since I can’t even imagine what connection it is supposed to have.  For the record, I no longer think it is insincerity, since you are sticking to it even after quoting the larger context; it must just be misunderstanding, so I withdraw this unflattering supposition.  You seem to be assuming I meant something completely different when I said “results” from when I said “fruits”, and you are doing something to one of words or sentences to give it a completely different meaning.  For the rest, I’m baffled.

Point 2:

I’ll admit that I was somewhat baiting you by “announcing” (instead making it clear that it was only a guess based on your posts) that you had not met evolutionary biologists and did not read their work.  This was rather a cheap way to get you to do your best to prove me wrong, and I apologize for not asking you directly.  Your response indicates that you have met one evolutionary biologist for 2 hours and that you’ve “read many of them”.  Happy to be proven wrong.

That said, the first part rather speaks for itself; if you feel you’ve earned the right to denigrate the work of the entire scientific field based on your 2 hour interview (in which you hardly sound like you played the role of an open-minded inquirer), then I would find that a little embarrassing if I were you and I wouldn’t trumpet it quite so loudly; this is not the testimony of an earnest seeker after knowledge and that two hour interview doesn’t even begin to cover your moral responsibility to “test everything and hold on to what is good” (especially in a highly complex subject where the vast majority of scientists disagree with you).  Maybe it is instead based on the scientific works that you’ve read, but you were rather coy about just what those works consisted of.  I said scientific works and I really meant to draw the line between that and the more popular works available to all.  Was there a materials and methods or a statistical methods section?  What was the name of the publisher?  Was it peer-reviewed?  The truth is, even if you plowed through some scientific papers (maybe you really did, please make me eat my words if this is so, it would be a pleasure to be debunked!), very few laymen would understand them in any real detail without the right background, so the real question is: have you studied evolutionary biology at a level higher than high school?  For how many years?  And just hypothetically speaking, how many years might be needed for you to feel you have performed your due diligence before dismissing the work and the results 99% of the experts in the field in question?  Humility would suggest that quite a few years might be needed before you should feel comfortable taking that route.  Pride would suggest all sorts of other things.  Or is there something else giving you such confidence in this matter?

It isn’t even just that 99% of those who are in a position to know and understand the field disagree with you.  It’s that the remaining subpopulation has a known religious bias against anything that they take to contradict the bible, meaning that you aren’t even free to assume some special level of objectivity in this tiny sliver of remaining experts.  But your confidence does not budge and the extent of your self-doubt is negligible. I don’t know what to call that, maybe “hubris” or something like it.  Having an opinion is normal, but its good to know when you wildly overshoot (though we all tend to overshoot our actual knowledge base in some pet-topic, be it weather patterns or sports or stock market predictions, so maybe what you are doing us just a normal human foible).

Part 3:

Thanks for making the effort to support the contention that the discovery of a common genetic code is that reason that evolutionists propose evolution.  As I previously pointed out, evolution was proposed and has been supported entirely independently of common ancestry, although common ancestry was always a possibility.  This doesn’t strike me as being controversial, yet your statement contradicts it freely.  So no, evolution itself stands and is habitually studied completely without allusion to the question of whether all life is related, which is a separate but related question.  Darwin’s showed very little interest in whether there was one or multiple original forms, all of his evidence provides no possible inferences on the subject and nothing in his works is affected by which happens to be the case.  I take that as being well established.  The fact that we all have a common DNA code is interesting, because there are apparently multiple chemically equivalent codes that might have been used and might
have been expected (to the probable advantage of the species that have them, negating the dangers of a large range of viruses etc), but either way, this fact does not itself necessitate the conclusion of common ancestry.  I would imagine that for some scientists who considered that there was a strong case for common ancestry before DNA was discovered to be all but universal, this discovery must have been viewed as a further confirmation (for some, this apparently “nailed it” as your quote has it), but I am unaware of anyone, creationist or evolutionist, proposing that the universality of DNA is the reason that evolution should be proposed.  Maybe this was just loose speech, and you meant something less ambitious than a direct DNA to evolution connection, but I find that creationist arguments are largely made up of loose-speech, redefinitions (like the ever vague creationist definition of “information”, so defined as to be impossible without a designer, or even neologisms like “historical/observational science”, where evolution is invalidated by definition), misleading partial quotes and a host of other linguistic sins, so I tend to zero in on such things. I think I have no reason to accuse you of anything other than loose speech at this point, and maybe loose reading (part I). Actually, I would now assume that you really must have had something different in mind than what you actually said.  If all you meant is that many evolutionists take the common genetic code to be further evidence of common ancestry, in combination with other (preceding) data, then I have no real quibbles with your point.  But any chance to clarify what you really meant was lost when it was further asserted that a close % commonality between chimps and humans was used to confirm common descent.  This is simply untrue and it would require a very muddled evolutionist to assert otherwise.  It’s not even clear what logic might be used to support this (which is why scientists don’t).  Your thinking just isn’t quite clear on this matter or at least your posts aren’t, though I did appreciate your efforts to investigate what is actually being asserted by evolutionists, and what you found was interesting.  It might be good to clarify what you really meant so that it could be decided whether it is a misconception on your part or a real evolutionist argument (it certainly isn’t as it stands).


g kc - #85980

July 15th 2014

GJDS - #85981

July 15th 2014

The enthusiasm and uncritical acceptance of Darwinian evolution by BioLogos seems to exceed that of most biologists, whatever their belief systems may be. Such uncritical acceptance is not found in other areas of the Sciences, whatever theory or paradigm is discussed. I have used the opinions of prominent evolutionists who maintain the intellectual rigor demanded by serious science, to show that many doubts and have many questions are made on Darwinian thinking. I provide another example below of a paper that summarizes the prevailing thinking on Darwinian thinking, and this questions the TOL concept, and proposes instead a forest of life.

Recognizing that a field (biology) is currently enamored by its Darwinian paradigm, is not the same thing as claiming the paradigm is sound, let alone proven; the views by many Academies of Science often are that it is the best available, and this is because a better one has not appeared on the scientific landscape (this is not a ringing endorsement but one that shows a better one is needed). I find it remarkable that after 150 years, Darwinian thinking has undergone more ‘face-lifts’ than any other theory of science, and yet biologists still cling to it with a touching reverence. My view as a scientist is that the bio-sciences are extremely complex, and as a consequence providing such an enormously overarching ideas is very difficult. It is the naivety and vast generality of Darwin’s outlook of variation and natural selection, made on an analogous basis, that I think has made it so appealing. As a theory that claims so much, it is woefully inadequate. In any event, another quote from an article that summarizes current thinking that covers the entire area (Koonin, SURVEY AND SUMMARY. Darwinian evolution in the light of genomics, Nucleic Acids Research, 2009, Vol. 37, No. 4 1011–1034):

“Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate

depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation.”

The impression offered by such papers show an obvious lack of a vast consensus claimed by BioLogos and others. However as scientists we should be cautions, in that our criticisms are not allowed to appear as if we are condemning all of those bio-scientists who believe in Darwinian evolution. Science has indeed progressed from inadequate formulations towards more adequate ones, and I am inclined to believe this is also the case for the bio-sciences. I think the clinging to what should be an outmoded Darwinian view is an impediment to the required progress in this area.


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