Why I remain a Darwin Skeptic

So @Shekar requested if I might share my own reasons for remaining so skeptical of the larger Darwinian evolution theory, and of EC, and why I am still sympathetic to ID. Here’s my initial outline of my thoughts, apologies in advance for the length. I’ll split this into a few initial posts to better organize. I welcome any additional thoughts, but this is mainly to answer his questions:


So first, a bit of background - I was exposed to traditional creationism / creation science when I was in high school (beyond that I was taught the standard Darwinian model and had never doubted it). Now I found creationism interesting, but I remained skeptical of it, critical and skeptical as I tend to be - one person I heard going on about the “odds” of even a single protein forming by chance… but that observation didn’t impress me much at the time - I remember thinking, “Sure, and winning the lottery is a ridiculous long shot as well, but if you have enough tries or enough people playing then someone is almost certainly going to win eventually. Given enough time and chances…” Also I remember being struck by the complexity of life that was shared with me by these folks, but still was aware of the competing theory’s responses: “Sure, such and such is complicated, but it didn’t need to happen all at once… minute variations, assisted by natural selection, little by little, over a very long period of time…” So I remained skeptical. But given maybe my skeptical (or tentative, or at best “humble”?) nature, I wasn’t sold as a devotee to either of those approaches. I think I kept a, “Let’s wait and see” approach for myself.

In college, though, when I started my Biology/Biochemistry major… I Began to get blown away by a few things:

–The RIDICULOUSLY intricate, detailed, programmed, multi-layered, molecular machinery and database of DNA,RNA,Ribosomes, & Protein Synthesis. Up to that point, I’d heard creationists talk about how complex we are. I had no idea we were talking this kind of complexity. I remember at the time being utterly blown away by that system. I had done lots of computer work previous to this, and recognized this design as being akin to that. I MEAN, THIS IS A FREAKIN’ DIGITAL 3D PRINTER! You have a (Read Only) essentially digital database, a system to read the data, transfer that data to the mechanical “printing” system, and then this ridiculously brilliant system for essnetially decoding, then identifying and utilizing the exact amino acids in order to properly sequence them. The whole system is more brilliant than anything I had ever come up with. It struck me that if mankind were given the task, given only what we know about molecular/organic chemsitry, to come up with a system that could keep a database of 1000 proteins and be able to transcribe and “print” them… it would prove an impossible task for us. Then the line I’d heard about somehow organic matter getting zapped by electricity or thermal vents or sunlight, then just somehow getting formed into these processes began to move for me into the realm of high fantasy. I realized in this process almost immediately after I understood it that it had something about it that came to be known later as “irreducable complexity”. I hadn’t heard the term or the concept before that, but I instinctively recognized that. For the system to work, you needed DNA. You needed RNA (and the process by which it gets copied). You needed a coordinated/coded system somehow for the tRNA to latch onto very, very specific amino acids (and only those) for the entire system to work; and then you need a very, very, very, very specifically shaped and designed ribosome in order to make the system work. You needed ALL of these to get anything. This is years before Behe’s first book, but I recognized what came to be known as “irreducable complexity.”

Beyond that, we did the standard biology 101 experiments on evolving fruit flies… and I studied the various “interesting” mutations that can occur, and started to realize they are either very small and pretty insignificant e.g., eye color (though perhaps would give an advantage to survival), or atrocious (like legs growing where the eyes should have been), but never seemed to be something one could ever start growing a new organism with.

Finally, what in my background started to increase my skepticism… one of my professors had done significant work with mutations and shared with us that he considered it impossible that mutations could have much to do with evolution - now he was an absolute Darwin devotee, but he shared that in all his work and knowledge, mutations just don’t do what is necessary. He attributed nearly all of evolutionary change to population genetics. It didn’t take me long to realize, though, that population genetics have an effect on changing what already exists in the genes, but it isn’t going to “invent” something new. I had a long talk with him about this, and it essentially ended with him acknowledging that, for his understanding to work, the DNA for every elephant, dolphin, spider, sea cucumber, and human would probably have had to have been present in that first cell, and population genetics just kept shifting all that information to get where we are today. I found it absolutely ludicrous, but he was happy to believe that. It was then that I started to wonder if the proverbial emporer in fact were wearing any clothes.



So all that background, let me try to outline my present skepticism. I read Behe’s first book some time ago, and recently read some of Stephen Meyer’s works, but most (though not all) of that simply confirmed my doubts from my own previous study, or gave me additional examples to those I had considered myself, but where I noticed the same pattern.

  1. MATHEMATICS - The one significantly “new” thing to me was in understanding just how unlikely we are talking. I’d never done the math before reading “Signature in the Cell.” I had brushed off my creationist friend’s “just forming one protein is so unlikely” claim by the “sure, but given enough time and opportunities” hand-wave. But Meyer’s book walked through the actual math involved, and I started doing some calculations myself. For a rather small, modest length protein of say 100 amino acids, there is something like 10^130 different combinations of such. Now of course, there isn’t just one solitary single sequence (or number) that will produce a certain biological function, but then common sense with my little science background suggested they can’t be practically innumerable, either. So to be generous, I speculated that perhaps there are 100 quintillion (100,000,000,000,000,000,000) possible combinations that would allow a certain biological function (some more effective than others, of course.) And then, let’s presume an ocean full of amino acids (from many fortuitous occasions of the Miller-Uray process), where we allow a trillion times every second, across the last 10 billion years, amino acids have just been combining, searching for this particular biological function… If I did my math rightly, this rather generous process allows only a 1 in 10^90 chance of finding said functional protein. We could increase the number of “functional combinations” of amino acids by a factor of another quintillion and the difficulty would remain. In Meyer’s book I recall he put it in perspective - it is somewhere in the neighborhood of someone picking at random a single atom in the entire observable universe, and then I also blindly pick the same atom. And only one shot. People have and can critize my assumptions, but have never been able to give me hard numbers (or even ballpark ones) that would change the basic difficulty here - but this is what gave me a sense as to the ridiculously huge difficulty in getting just one fraction of these processes right, not to mention the layers upon layers of integrated complexity needed for life to work.

  2. BACTERIA / VERTABRATE GENERATION EVOLUTION COMPARISON - I at one point also turned my mathematical analysis to comparing evolution across species. I noticed, for instance, that it is believed that in a (mere) 10 million years, or 1 million generations (given ~10 year generation time in dolphins and whales), echolocation developed in whales/cetacea, along with a new specialized organ to aid that process. But if I expressed skepticism about that, that we don’t observe such complexity forming in this process, I was always told that it is just too slow for us to see. We can’t observe a million generations of whales. It occured to me, “Why not look for an analogous process in a species we can observe for over a million generations?” and it occured to me, since the invention of microscopes capable of observing bacteria, we have been able to observe and document organisms like e coli over the last 50 years or so. In ideal conditions they can reproduce every 20 minutes or so. In the most ideal conditions, that is around 25,000 generations in a year, which would allow potentially somewhere close to a million generations across billions upon billions of organisms in 40-60 years. Again, people can challenge specific assumptions, but the basic observation doesn’t change:

Simply put, the process I am asked to believe that hasn’t produced even a start of any new organelle in an organism we’ve been watching for 50+ years, that has huge population sizes to work with, and is relatively benefited from occasional mutations… that same process that has done essentially nothing while we watch it over a million generations, somehow magically created a new organ and rewired existing systems to create pinpoint accurate, directional, fully integrated echolocation system in essentially the same generation time, with a much smaller population size, in an organism less friendly to mutations.

And when I point this out, there are all sorts of what sound to me excuses, goalpost-moving, hand waves, special-pleading about why this doesn’t work. “Oh, that process works wonders in a million generations for vertabrates… but in bacteria, those achievements would need, um, let’s see… 100 billion generations. Yeah, that would work…” Sounds almost like Dr. Evil moving the goalposts. Or the kid from mystery men that could turn invisible… so long as no one was watching. Evolution only happens on timeframes that are too long for us to observe… and that timeframe changes depending on our ability to observe.

So my skepticism remains. The same process that magically gave us a fully-integrated, perfectly designed, functionally specific new organ in a million generations in a species we can’t watch that long can’t give us even the most minute beginnings of a new organelle in the species we can watch that long. It is a bit too convenient for my taste.

  1. ENGINEERING PRINCIPLES - Now, if I haven’t said it earlier, I have no difficulty whatsoever with the basic principles of what is called microevolution. but even in the engineering world, there are “improvements” to basic systems, where the basic system remains intact, and we continually make new upgrades, and radical overhauls that simply can’t be done by a series of minor adjustments. The propeller driven P51 planes of WWII could theoretically be traced out as the “ancestors” of our modern turboprop planes, more or less. A slight increase in propeller speed here, a fatter wing there, etc., one can appreciate how a series of slight changes can make basic improvements to a system (or better adapt it to other environments), while the essential system remains the same. Modified bird beaks, etc.

But much of “macroevolution” entails such major overhauls… turning the principles of flight into an Osprey VTOL is simply something you can’t do by making a series of minor modifications… The system works one way, but to make the propellers function to give both forward and vertical flight is something that is remarkably precise, and has to be done in just a certain way… and trying to get to it by numerous slight modifications of preexisting plans is simply doomed to failure - at some point trying to modify a regular fixed wing to get to a tilt-wing will result in endless crashes before you ever get something that will work.

Transforming a regular flight bird into a hummingbird would be comparable - a hummingbird’s design is so ridiculously precise, integrated in so many parts (neurological, wing structure, digestion, instinct, etc). to allow it to hover with such precision or flap wings with that kind of speed. Everything about it suggests to me it is not the kind of endstate that could be achieved by a series of random variations, however assisted by natural selection. I could conceive of a sparrow evolving into an eagle by a series of such modifications - though I still think a bit far-fetched, it doesn’t seem out of the realm of reality altogether… while rather different it seems in general variations of the same aerodynamic principles. Hummingbirds use a radically different flight engine, one that I have a very hard time seeing any possible pathway that random, minute changes could get from one to the other, however assisted by natural selection, unless they were very specifically chosen and intentionally designed changes. And lots and lots of other examples like this.

Echolocation is like that to me, also. Dolphin sonar is so ridiculously precise, directional, with immense ability to discriminate objects in water that are beyond our best science. An ability that arose in a mere 1 million generations from essentially nothing. Some have told me that all hearing mammels have a nascent ability to echolocate, and that this was just continually modified. To me that seems a hand wave ignoring the tremendous engineering challenges involved. I could likewise say that "Any ship can find the ocean depth… Just put your ear in the water, bang the side of your boat with a hammer, start counting “1 onethousand, 2 onethousand,” and time how long it takes till you hear an echo. OK, fine. But saying that this process gave rise to our modern fathometers would be ridiculous. echolocating cetacea have specially developed new organ that sends directional high-frequency clicks, and has an array system to allow them to precisely determine the exact direction (not just left/right/straight like we do), and does so in the aquatic medium where sound travels like 4-5 times faster, etc.

So finally, when I express astonishment at certain marvels of design in life, I feel like the response is essnetially to hand-wave these observations aside, with the appeal to “well, just lots of small changes…” But I know certain engineering marvels don’t happen like that. We can “tinker” with the design submarine nuclear propulsion to make various and sometimes impressive improvements… but we didn’t get nuclear propulsion by continually tinkering with the design of our diesel-electric submarines. Sure, there is lots to carry over (both might use shafts, propellers, hydrolics, etc.), but the propulsion system is entirely a brand new design.



OK, To finish up… It is not lost on me that any atheist scientist is compelled to find a naturalistic process by which human life happened. If there are some aspects of life that are, in fact, too complex, too intricate, too precise to have ever happened by chance mutations helped by natural selection, an atheist scientist will never acknowledge that. They can’t. Their worldview precludes this as something even to consider. They will seek, find, affirm, and defend a strictly natural process. Even the hypothesis, “This may be too complex to be explained by any natural process” is impossible to allow. An atheist scientist simply will not and can not ever recognize any biological phenomenon as “too complex” to have happened naturally… even if by some chance this were the truth case in any particular case.

So when an atheist scientist says that he has exmained some especially complex biological feature, and come to the conclusion that it evolved by a natural process, this is exceedingly uninteresting to me. Of course he was going to conlcude it could have happened by a natural process. The same scientist will say the same about Jesus’s resurrection, that there is a perfectly natural explaantion for it. But I am listening to someone who is essentially begging the question - He starts with the assumption that only a natural process could have produced this, and concludes by saying this was caused by a natural process. Big surprise.

My biggest challenge, difficulty, and complaint about EC as articulated by Biologos is that, in embracing Methodological Naturalism, they put themselves in exactly the same position as said atheist scientist. So long as they are following methodological naturalism, they will seek, find, affirm, and defend a strictly natural process - however much they might acknowledge that God’s hand was “somehow” behind it, that there is no hard/fast boundary between natural and supernatural, however much they credit God’s overarching providence… they simply would not and will never recognize any biological phenomenon as “too complex” for it to have happened “naturally.”

This, similarly, is supremely uninteresting to me. In fact I am a bit blown away that their own stated self-description is about as plainly stated a question-begging fallacy as one could ask for: “At BioLogos, we believe that our intelligent God designed the universe, but we do not see scientific or biblical reasons to give up on pursuing natural explanations for how God governs natural phenomena.” OF COURSE we should pursue natural explanations to natural phenomena. But the very question at hand is as to whether or not a certain phenomenon is, or isn’t, a “natural phenomenon”… or in contrast, if it may be the result of intelligent or purposeful agency. Begging the question by assuming the conclusion (i.e., affirming/assuming a priori that such and such phenomena are ‘natural phenomena’), and their failure to recognize how this is obvious question-begging, only increases my skepticism for the approach. They will arrive at a predetermined naturalistic conclusion, and their inability to recognize that this conclusion was predetermined by their philosophical commitments makes me extremely dubious in this approach as a means to determine what is actually true.

So, as you very well stated earlier… “…in the face of the evidence we have, biological evolution is more parsimonious, has more explanatory power, etc. You don’t need MN to make this case.” THIS perspective is very much worth engaging. I feel I would be talking with someone with an open mind, able and willing to follow the evidence wherever it leads, looks at evidence involved, and concludes with an entirely open mind that it bears the hallmarks of having evolved by natural processes; that natural selection operating on random variations could accomplish this by such and such reasonable and not unlikely pathway, etc., etc. That I would be very interested in listening to. But far too often when I am speaking with someone who has embraced the Methodological Naturalism approach, I can tell they simply would not acknowledge something as bearing the hallmarks of design even if it had every conceivable hallmark of such.

Finally a theological observation. I have tried, very deeply, to consider if I could accept the basic evolutionary/EC viewpoint by harmonizing it with what I already believe about predestination and providence. The book of Esther, the details of Joseph’s life and God’s plan behind it, I could give example after example of things that were clearly God’s doing, purpose, design, and intent, but which would be, essentially, indstinguishable from the “regular” course of nature. There was nothing “supernatural” recorded in what Joseph’s brothers did to him… no miracle was needed for his brothers to kidnap him, no divine intervention was needed for them to sell him to slave traders en route to egypt. But nonetheless we can affirm with Joseph, “God intended this.” God was working, planning, designing, purposing this, but doing so in a manner that was essentially indistinguishable from how the regular course of nature was progressing.

I’ve tried to go that route - could that be how God is working with evolution? could he just, in providence, be working out a beautiful plan, bring about the marvels of the natural world, and the wonder of humanity, by what seem serendipitous circumstances, such that when we examine them, they seem in every way “natural,” but clearly God had a purpose and design “behind the scenes”?

But try as I may, I simply can’t go there. There are fortitous things, and things that are beyond obvious that they require direct intelligent intervention. I go back to a basic analogy - Let’s say I invited you over to play poker, and you noticed that 6 times in a row, every time I dealt, I happened to deal myself a Royal Flush. You object, and suggest that I am cheating.

I say, "Now, remember, God is at work in and behind all things, and in his providence, this is just how God is working ‘behind the scenes.’ Just because there was an extraordinary outcome doesn’t mean we have to impute some kind of direct, intelligent agency. Yes, just like EC, God is at work and guiding and directing, but in a way that is indistinguishable from nature. 'I see no see scientific or biblical reason to give up on pursuing natural explanations for how God governed this natural phenomenon…’"

You wouldn’t buy it, of course. There comes a point where certain outcomes are just so extraoridnary, or so otherwise impossible, so intricate, that “nature,” even trusting as we do it is ordered by God, simply is not an adequate explanation - any more than the entirely natural processes of card shuffles and related statistics - even acknowledging God working in and through the natural world - would be an adequate explanation for my 6 royal flushes.


Finally (last point for now I promise)… people talk about “how similar” human DNA is to that of chimpanzees. Only a 2% difference, I understand. Sounded impressive to me, again, until I started doing the math… 2% of 3,000,000,000 (base pairs) is 60,000,000 differences in our DNA. Doesn’t seem quite as small to me when it is stated that way. Wikipedia tells me we have around 64 mutations per generation. HCLCA and humans diverged maybe some ~700,000 generations ago or so. Getting all the right mutations to make us what we are seems very, very fortuitous.

All these random mutations operating with natural selection in what, evolutionarily spekaing is a blink of an eye (mere 6-7,000,000 years with 10-15+ year generation times) had to stumble upon just the right changes to make us what we are. The just right random mutations had to come along to perfect human language, ingenuity, intelligence, art, etc. The differences between chimps and humans I find to be so terribly minimized by those wanting to defend the naturalistic evolution between them - Of those 60,000,000 mutations, just the right ones had to happen, be selected, get solidified in the gene pool, to give us the ability to speak hear and understand multiple languages, to read, to write, to hear, appreciate and recognize minute frequencies such as to appreciate music, to play music, to make art, to memorize and perform reams upon reams of music, to do calculus, build space shuttles, write poetry, etc.

Talk about dealing multiple royal flushes in a row. Everything about it appears to me as if the deck was stacked.

OK, I threw a lot out there… sorry for the book, but that should give you plenty to choose from to ask about to further the conversation. Hope that answered your question and gave you something to work with to further the conversation - Please feel free to focus the discussion on one or a few of the items I shared there - I gave a lots so you’d be able to choose from any of those topics to discuss in further depth as you so desire.


Until there’s a scientific alternative to the Darwinian synthesis, what else should I believe?

You could always believe that the truth has not yet been discovered, of course. That is a very valid position. One can disbelieve theory A or recognize it to be faulty in various ways even if you cannot (yet) offer or embrace an alternative, no?

What truth? What’s missing? Nothing in physicalism.

There is a scientific alternative. It is called ecological evolution and it has shown to be true many times as in the extinction of the dinosaurs.

Hi Daniel,

Thank you for the time and effort you put into answering my initial question. I will go ahead and start with Human Evolution.

So the first thing I would like to understand is whether you would think it to be the case that humans share a common ancestor with chimpanzees/bonobos?

What you say sounds like you either accept or are willing to accept common ancestry between humans and chimps/bonobos that was directly/‘strongly’(?) guided by God (at least in certain respects)?

Very good and apposite question. Briefly, it depends in part by what we mean by “common descent”… I don’t harbor nearly as strong an objection to biological/reproductive common descent itself as I do to the supposed mechanism of common descent… whether in human ancestors, across Other species, or all the way from an original single-called organism to man. I have my reasons for doubting it - partly because there seem to me alternate legitimate hypotheses (which I’ll outline below), but my doubt or rational objection is not nearly as strong as to the “random mutation + natural selection” mechanism itself.

But if by “common descent” we mean it in a broad sense, I essentially have no objection whatsoever…

  • Firstly, common descent is largely predicated on the supposed mechanism of small, minute variations accumulating and directed by natural selection. If this were somehow fully disproven, at least one plank of the larger biological common descent hypothesis would be removed.

  • that said, I can conceive the basic logic of a process (I believe as embraced by Behe) where God (or whichever designer) allowed evolution to proceed, but then at various points introduced by some direct manner certain radical, fully formed, complete innovations. I don’t have any particular rational or scientific objection to this hypothesis, as I do the blind natural selection/random mutation mechanism.

  • Thirdly, though, I could conceive, hypothetically, of a process wherein the essential design or blueprint of any certain organism was a starting point, and a designer made heavy modifications (mentally or otherwise) to the design, and created new organism de novo, but with heavy reliance on previous design, making required modifications. (This, and the above, seem like they would be relatively consistent with the “punctuated equilibrium” hypothesis of Gould, by the way).

  • also a bit odd, but variations on the above, I could conceive hypothetically of the design going in the reverse… that man could have been the first organism conceived, then as the design process unfolded, we kept modifying that template to achieve the lesser organisms. Or even many various designs informing each other all at once.

The third bullet above by the way is essentially how we do things in the engineering world. I can walk through various classes of submarines, and see lots and lots of identical components, systems, structures, designs, etc. Or one could do it with automobiles. obviously one can take a bunch of automobile designs, examine them in detail, and perceive and outline The “common descent“, based on introduction of new features, vestiges if previous designs, etc… obviously they didn’t have common descent in the biological/reproductive sense, but one could recognize such common descent.

I’ve observed the same in computer science. I can still (on windows 8 on my PC) pull up files that are vestiges of good old windows 3.1 back in the 90s. My favorite is “moreicons.dll”, which I often used to select different icons back in windows 3.1… and which I can still use for more icons to this day in windows 8. and half the icons reference “MS-DOS.” a vestigial item if I’ve ever seen one!

So yes, I’m the broad sense, there is unquestionably some kind of “common descent” in submarines, automobiles, and software programming. And I would wholeheartedly endorse the same in biology. I remain a bit dubious of the core biological /reproductive common descent, only because, logically, we’d have to somehow remove the other competing hypothesis (of common design). And the other half of my skepticism comes from the fact that scientists… whether atheist or EC/MN devotees, would not even be willing to consider the other alternatives for the reasons I discussed above. I’m not willing to toss out such hypotheses so quickly. Again, they seem to be very much predisposed to only see biological common descent, as they have essentially a priori ruled out alternate hypotheses from consideration, as previously discussed.

But in short, again, no, I don’t have a very significant scientific or logical objection to common descent in any kind, including the hypothesis that a single cell was started and through whatever processes was adapted, and changed, and eventually became us people. My core scientific objection is almost strictly in the attribution of that process to the unaided random mutation/natural selection process as having the ability to achieve such changes.


Link? To science of course. You are the only person who uses that term.

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Why I remain a skeptic of the value of discussions like this?

If people want to believe in fairies, ghosts, UFOs, psychics, healing crystals, necromancy creating golems of dust and bone, vampires, magical fruit, mermaids, talking animals, or that the earth is flat, then they are going to believe in them. I don’t see the point of participating in their delusion even to point of being drawn into a discussion with them. I came to this site because I was sick and tired of it. It’s time to move on to the discussion of what these discoveries of science mean for Christian theology. Let’s leave the dark ages back in the previous centuries for it is insanity to resurrect this age of filth, sickness, poverty and human abuse.

No one doubts except perhaps Dawkins that ecology is a science. On the other hand ID is not scientific per se, nor is EC. Karl Popper rightly said that natural selection as survival of the fittest is not scientific.

All I am saying is that ecological natural selection is based on verified science, such as symbiosis and the extinction of the dinosaurs, even if scientists do not accept it.

I studied ecology at university. I didn’t come across it then. And 45 years later, one still doesn’t.


Ok, so I would like to know what you think about things like the following,

1) Whole Genome Duplication

2) Horizontal Gene Transfer

3) Transposable Elements

4) Polyploidy Rapid Speciation

5) Endosymbiosis

The reason I bring these up is for three main reasons,

I) Many challenge evolutionary gradualism. That is they provide possible mechanisms to understand something like punctuated equilibria as observed in the fossil record.

II) Depending on how you think about ‘random’, something like transposable elements allows for adaptation in response to environmental conditions.

III) Evolutionary processes can differ between organisms.

Something all this suggests to me is that they cut against your e-coli/dolphin comparison. They are different organisms and do not necessarily undergo the same evolutionary processes which makes comparison between them more complicated than a simple generation/adaptation comparison. Also different environmental contexts can have different evolutionary results.

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Appreciated thoughts. I’ll need some time to read through and digest everything, in order to give a proper response. Thanks for all the thoughts. Will get back to you soon as I can.


This falsehood is typical of the author of this post (@Relates) and it’s shameful. To repeat this falsehood after it’s been called out, multiple times, is to openly disrespect the other participants in this forum. To other readers: @Relates doesn’t tell the truth about Dawkins’ ideas. To boot, the falsehood dodges the question that was asked, which I can answer: there’s no such discipline as “ecological evolution.”

That fallacy is what you see looking down the wrong end of the telescope.


Why is that generous? It’s equivalent to saying that only 1 out of every 10^110 combinations that would have any function. What justification is there for making such an extremely ungenerous assumption?


As anticipated…

Are you familiar with search algorithms in computer science, Daniel?

“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6

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