Evolution: The Untold Story, Part 1

There are two kinds of evolution:

1) There’s the version that you read about in the bookstore. It’s two-thirds science fiction.

2) Then there’s the version that PhD biologists, cancer researchers and genetic engineers use to do their jobs.

The two are entirely different.

Popular books tell you evolution works like this:

“Mutations are the random changes in genes that constitute the raw material for evolution by non-random selection.”

-Richard Dawkins, The Greatest Show on Earth, 2009

Dawkins would have you believe that all you need is the fantastically amazing power of natural selection, and given enough time, through random copying errors, the most extraordinary things become possible.

This is what casual bookstore readers and college freshmen are told. But it’s ridiculously oversimplified and it’s mostly false. It’sdick_and_jane the “Dick and Jane” story of Evolution.

But there’s another version of evolution:

It’s rarely mentioned, or at best glossed over, by the atheist evolution lobby and the mainstream press. Yet it’s incredibly sophisticated and elegant. This is “Real World” evolution.

As you begin to discover Real World Evolution, you find it’s entirely different from the Dick and Jane story you were taught. 98% of people know nothing about this. Today, the first in a series where I share with you the incredible adaptive engineering that’s under the hood of all living things.

Evolution Untold Story #1: How Bacteria Adapt

You probably know that bacteria develop resistance to antibiotics. The more we use antibiotics, the more resistance bacteria develop and the harder it is to kill them. We all know that we must not over-use antibiotics. But has anyone ever told you how bacteria generate this resistance in the first place?

Hint: It doesn’t happen by accident.

You’re fighting off an infection and you’re taking antibiotics. To the bacteria, the antibiotic is poison. It leaks into the bacteria cell wall and begins to kill it. The bacteria says, “This poison is killing me. I have to find a way to pump this out of my system!”

It travels around in your body, hunting for a pump.

It locates a cell somewhere in your body that has a pump. It extracts a copy of that cell’s DNA from a plasmid. It locates the section of the new DNA that codes for a pump, inserts that code into its own existing DNA, and builds a pump.

This is called Horizontal Gene Transfer or HGT. It is one of the most common evolutionary mechanisms. This is “real world evolution.” It’s been observed in labs for 50 years now. Because of HGT, the traditional evolutionary “tree of life” isn’t really a tree, especially among lower organisms. Because of genes being passed back and forth between organisms, it’s more like a web.

If the new pump does its job, then the bacteria can now resist the antibiotic. It now produces other bacteria that inherit the same resistance.

But it also does something else: It finds its bacteria brothers and sisters in your system and gives them the same piece of code!

Now ALL the bacteria in your system have a pump that makes them immune to the antibiotic. Your only chance is to find a more powerful antibiotic or hope your body can find some other way to kill them.

Horizontal Gene Transfer on Video:

Consider what Horizontal Gene Transfer tells you about bacteria:

1. They know what new features they need to survive attack
2. They actively seek out other organisms with those features
3. They exchange and read the DNA of other organisms
4. They analyze the DNA of those organisms
5. They locate the sections of DNA that they need
6. They splice the correct sections of DNA into their own DNA
7. They build entire new complex structures with the instructions in that DNA
8. They evaluate the success of what they’ve done
9. They pass the adaptations along to their offspring
10. They evangelize the newly acquired code to their fellow bacteria

Notice that this does not take thousands of generations. It takes one! Through HGT, an organism can acquire a completely new feature in one step. No gradual accumulation of errors necessary.

Bacteria are not stupid. Invading organisms stage an attack, an arms race against your immune system. Bacteria are as skilled at using code as as any software programmer you’ve ever met.

Hmmm… what tricks could software engineers pick up by studying bacteria?

Your own immune system fights back the exact same way. When you get an immunization shot for tetanus, for example, a weak version of tetanus is injected into your blood stream. Your cells have to “crack the code” of how to kill it. Once they’ve done so, they pass this information to their offspring.

You need to get a new immune shot every 10 years, because after a long periods of time, if your immune cells don’t need the extra code, they’ll discard it. Your cells won’t carry around extra instructions they don’t need.

Single-celled organisms are capable of exchanging DNA with each other, and HGT is massively influential in the development of living things. My friend, Open Source Software is w-a-a-a-a-y older than Linux. It’s been powering nano-machines for 3 billion years!

Organisms share code much the same way musicians and writers and software engineers share riffs and rhythms and programs. The never-ending arms race between prey and predator makes each incredibly robust and ensures the survival of both.

Are you beginning to notice how entirely different this is from the antiquated “random mutation” theory? There’s nothing random about Real World Evolution at all. It’s spectacularly sophisticated. It’s intentional.

The “Dick and Jane” version of evolution is deeply misleading, because it fools you into believing that as long as cells replicate, evolution is somehow inevitable. That it’s bound to happen sooner or later. People try to tell you that natural selection is capable of cleaning up whatever mess is made by haphazard, purposeless accidents.

Not true. Even the most elementary mechanisms of evolution – like Horizontal Gene Transfer – are extraordinary feats of software programming genius. Natural Selection has no creative ability whatsoever. It’s just the final step after the cells have performed their task of innovation.

Organisms evolve much the same way human ideas evolve: By intentional innovation and necessity. By borrowing and recombining existing ideas from the outside to form new ones.

If you’ve witnessed the evolution of English or jazz or computer software or smart phones, then you also understand biological evolution. Because all these things evolve through an identical set of processes: Intentional lending, borrowing, and re-combining of the old to make something new.

By the way, geneticists and other professionals who do cancer research and artificially modify organisms do not splice DNA with a tiny set of tweezers. They employ Horizontal Gene Transfer and other mechanisms I’ll discuss in this series. Scientists set up the experiments, but the cells themselves do the heavy lifting.

And while evolution certainly makes many “fortunate discoveries,” they’re not “accidents” in the usual sense of the word. No more than Thomas Edison’s discovery that carbon is a good filament for a light bulb was an “accident.”

Edison’s light bulb was no accident! He swapped out thousands of materials until he found one that worked. Organisms exchange genes and chromosomes until they find genetic combinations that serve their purposes.

Horizontal Gene Transfer is just one of several amazing, systematic evolutionary mechanisms. It’s not random or accidental, it’s algorithmic. In future installments I’ll share 5 more with you. Stay tuned.

Perry Marshall

Bacterial Conjugation on Video:

National Science Foundation: “One step at a time!” Do organisms change slowly or by leaps and bounds?

Citizendium Encyclopedia: Horizontal Gene Transfer

HGT via Parasites: How Bacteria Can Transfer DNA Between Animals. That’s right – micro-organisms can transfer DNA from one species to another. From Medial News Today.

124 Responses

  1. Paradise Holding says:

    Hello- you have not addressed anything as beginning. You have taken what is and applied it to the end result. Beer, wine ,and opioids were readily available 6000 years ago. Faith is belief based while reason is knowledged. Death is terminated (cellular activity) 24 hours after the body stops breathing.

    • Old Git Tom says:

      Mr(?) Holding,

      many people make the mistake that there is some clear division b/ween belief/faith on one side, & certain knowledge on the other. There is only a very foggy, un-signposted border!

      Science is mathematics-based. Centuries ago, scholars recognized that math requires trust/belief in ‘postulates’ – basics, things that are themselves beyond proof.

      Empirical, experimental proofs? Same problem, long recognized. What we ‘perceive’ is not some ‘reality’, but mysteriously-generated impression-data in our heads.

      Certainly some knowledge is more reliable than other kinds, but for that we usually apply the test of consistency. Does the evidence stack up, or contradict itself? But that only leaves us with degrees of probability in key areas. OGT

      • perrari says:

        Tom, I agree there is no universally accepted ‘certain knowledge’. One may say 1 + 1 equals 2, but that is not always true in all circumstances. However that does not mean that perfect, certain knowledge does not exist.
        If God exists then perfect knowledge exists.
        Man has 4 basic defects that prevent him from acquiring perfect knowledge by his own endeavors.

        However if perfect knowledge is REVEALED to him from a perfect source then he can know things beyond all doubt. He may not be able to convince others of the knowledge that he has received, but he can try to convince others to accept the process by which the knowledge was revealed to him.
        Amongst other things it requires faith, humility, patience, determination, a competent teacher and an open mind, and then each individual who accepts the process can know for certain what is true, as the Lord will reveal the truth to him or her.
        Empirical, rational, experimental, logical attempts to find the Absolute Truth will fail. But the revelation of the Absolute Truth Himself to an individual removes all doubts instantly and permanently.
        Such lucky souls who have these experiences and realizations tend not to shout their experiences on facebook and twitter, but reveal them only to serious and mature seekers after being satisfied by the persons sincerity and discretion.
        As far as I know, this is the only way to know anything for sure in this world of imperfect senses and illusion.

        Please try it.

  2. Dennis says:

    Dear Perry

    I accept that DNA is information and your beliefs are okay, except for your time element. You don’t deal with three elements that the Bible is clear about. The first being, death came as a result of sin, the disobedience of Adam and Eve. Therefore man existed before there was any death. Second, the genealogies of the Bible give us approximate dates for the flood, and even for creation itself. it is somewhere in the range of 6000-10,000 years, and closer to six, certainly not millions of years. Third, the creation account in Genesis supports this with six days being mentioned as the length of time for the initial structure and creatures to originate. This is backed up by the creation of plants on the third “day” with the creation of the sun (moon and stars, at least)on the fourth day. Without the sun, there would be no photosynthesis and therefore to place millions,thousands,or even hundreds of years of evolution into this interval is totally unacceptable.
    Now you don’t have to believe the creation account as fact, but you can’t call yourself a “Bible Believer” if you don’t.
    I do believe that this planet originated approximately 6-10 thousand years ago. This, of course, does not negate the possibility of punctuated programed equilibrium-type evolution as you present it, according to predetermined algorithms. It just means that under certain conditions evolution would progress more rapidly, as for example, in a world-wide catastrophic climate changing event, such as a world-wide flood as documented in the Bible. Of course, I expect that you have considered this. So please enlighten me.

  3. Dennis says:

    Dear Perry

    your algorithmic control on evolution makes sense, but how exactly does one species become another? Variation is observable, but a macro-evolution mechanism has not been demonstrated so far and may not be present in the algorithms. Corn is still corn!

    BTW, I’ve read your Genesis exegesis. Could be, but I think not. Where is the incorruptible body of Jesus Christ right now? Where is Heaven? Where is hell?

    Are they symbolic?

    • Old Git Tom says:

      Darwinism has no coherent explanation for speciation’, or as I (& probably Perry Marshall) would prefer to put it, the appearance of completely new designs of living things. The answer to this is a large mystery, the mystery of creation.
      Without scratching our heads too much, we can ask questions to which no-one can provide answers. The trick of science is to address problems to which answers can be found. But as I’ve said before, even science demands faith. The mathematics that so much science is based on, demands faith in the ‘reality’ of numbers that exist nowhere outside human minds.

  4. Kevin says:

    Correct me if I’m mistaken, but you are equating the hypothesis of evolution with the adaptations of individuals of a species–which of course are marvels of nature.

    You are not equating evolution with “macro-evolution”, are you? That is, you do not subscribe to the idea that over time species can transform into other species.

    And more particularly, you are not saying that species evolved from a chemical mix to a single-celled entity to produces the thousands of past and present species.

  5. Old Git Tom says:

    Darwin observed micro-adaptation taking place, or as we might say, minor design changes occuring. His final theory was that a long sequence of minor changes could amount to a major design change – speciation – the emergence of a new species.
    There are several fundamental problems with this theory, why it is now widely regarded as unviable.
    1/ Subsequent research of physical evidence does not give support. The great bulk of fossils show stable designs over very long periods, then sudden ‘jumps’ as they are supplanted or joined by new species.
    2/ Darwin was aware of both micro & macro evolution, but could offer no explanation of how one could ‘magically’ become the other. He hoped (in vain) that subsequent work would reveal a majority of ‘transitional forms’ amongst fossils: no, they remain a hypothetical chimera. AFAIK, modern science still has no explanation of the mechanism of speciation.
    Last, Darwin offered no theory as to the first origin of ‘life’. In fact, insofar as Darwinism remains a materialist outlook, it cannot, a priori. It demands an iron curtain between its two logical categories of life & matter. Having eternally & irrevocably separated the two, it can have NO WAY of explaining the emergence of one from the other.
    Of course, later theories have tackled the above problems, but then they are not Darwinism.
    Put another way, positing two states, life & matter, must result in a dualist theory (a la Descartes). Darwinism is a one-state theory – monism. As such it is unable, in principle, to explain the very mystery it attempts to address. Only by breaking & destroying the theory can monism become dualism. Hence, Darwinism is permanently wriggling on the horns of its self-made dilemma.

  6. Kevin says:

    Thank you for your reply, Tom, but I think I didn’t express myself clearly. I merely wanted to know what you meant by the term “evolution”. I wanted to know if you meant by evolution either

    1. what is commonly known as “microevolution”, namely the simple and observable idea that species are able to adapt–within limits, of course–to their surroundings and conditions, and are also able to be modified by selective breeding. This has always been known, of course.


    2. What is commonly known as “macro-evolution” or “transformist evolution”, namely the notion that species descend from a common ancestor and that, through random mutation, natural selection, genetic drift, etc., can transform into other species.

    It was just a question, that’s all, and not a brief one way or another for a theory of evolution

    • Old Git Tom says:

      sorry, I’m not sure if I can answer your question succintly.
      First, let’s set aside Darwin’s inadequate & obsolete theory of natural selection. It fails at several key points.
      Beyond, AFAIK, ‘evolution’ means ‘change over time’ – nothing more or less. But if time is s/thing other & separate from change, I’ve never u/stood how.
      So we have change=time, & time=change, yes? We NEVER see time itself, just changes, like day into night, youth into old age, moving hands of clocks, etc., etc. If you accept this, then there is no quick answer to ‘do you accept micro/macro evolution theory?’
      For me, evolution is just another name for the profoundly mysterious nature of time. My view is that time is eternal creation & re-creation. We can never see time or creation themselves, since we are closely-involved participants in their activities. Some might say that there is never a/thing new – time is just endless cycles of the same. I’d disagree; simply becoz, if there were never a/thing new, nothing would change, & we would have no time.
      Put another way, we know time destroys (entropy). We don’t fully perceive time as continual creation. Some call that evolution, but most never clearly see this hidden part.
      Hegel believed the knowledge of our mortality is the price we pay for conscious intelligence. Allegedly, most animals don’t have either.

  7. Kevin says:

    By the way, a little suggestion:
    make the place to login visible on the blog, instead of being hidden in the contact page.

  8. Carol Sperling says:

    Interesting read – the experience of Carl Zimmer having his whole genome sequenced and examining it in detail: https://www.statnews.com/feature/game-of-genomes/season-one/

  9. Matjaž Horvat says:

    I can see a Young Earth Creationist replying to evo devo theories by pointing out to baraminology: http://www.creationresearch.org/crsq/articles/43/43_3/baraminology.htm

    If it turns out that evo devo can only account for ‘mere’ speciation, and not what they call ‘biblical kinds’ or ‘baramins’, they may well use this as fuel for their theory. In fact, I think I’ve read an Y.E. creationist article recently claiming evo devo fits into their views.

    I predict creationist baraminology is only going to grow due to evo devo.

  10. Wim Stevens says:


    I’m a 47 year old Belgian computer scientist and owner of a software company. I read some of your work and I agree with you that DNA has to be created. If you look at the logical and algorithmically processing driven by digital code within and between cells than you need an information processing system between this data and its output, how could it otherwise be possible?

    A small example, how does a cell know where and which gene is to be fetch in certain circumstances without knowing its content or location? We are talking about 30.000 genes with a specific location and content, random chemical reactions will never end up at the right gene, this needs precise addressing! And now we don’t talk yet about the algorithmic processing afterwards.

    Further, DNA is a system that works in the same way through all living things, you can bring in genes from fish and import them in plants and it works! This means that this system doesn’t evolve otherwise we would have different non compatible systems running next to each other. So in this there two possibilities; either this system, (DNA), has been created some time in the past or somebody has stopped it to evolve further.
    Anyway, I’m also very sure that the underlying mechanism of all biological life is created and its phenotypes are evolved.

    What or who created it? I really don’t know but I don’t think that this instance proficient in advanced nano- and information technology would talk to us through clouds, voices, stone tables or brambles. I also don’t see any favourite treatment or interference from nature towards humans compared to all other living creatures, We all follow the same natural laws and there is no influence of our moral actions in surviving. A nun can die young from a terrible disease and an ex-nazi can become 95 without much harm. Nature is indifferent towards our fate. Thus I’m atheistic in all by men made up religions and there are a lot.

    So what can it be? My best guess is that this world is one big simulation run on a mega mainframe developed by a very advanced civilisation for experimental purposes.
    In a simulation a lot of odd natural laws become more logical, e.g. gravity is just a calculated algorithm and so is time and space. This also solves the question in quantum entanglement why one particle distant from another can change from state simultaneously. There is no distance, they just share and link to a same data field.

  11. Ashwin Sasidharan says:

    I have been reading up on the third way of evolution. Its definitely interesting. However, it seems to shift the problem by a step.If bacterial evolution is “algorithmic”, then its worth asking how the algorithm developed. Processes such as HGT, conjugation etc are extremely complicated processes.
    Have you heard about conservation of information? Though complicated processes such as HGT, Endosymbiosis, etc seem to make evolution more probable than “random mutation”.It really doesn’t. The information problem still persists in that “nature” needs to generate the information or algorithm in the bacteria that allows it to re-engineer itself.Have you read about the search for a search problem as described by Robert Marks and co in the evolutionary informatics lab? The bsic idea is that tools that make a search easy (like maps), themselves need information to be found. So that the total information needed is the same as requried for a blind search(like random mutation).
    Unless there is an inherent property to “life” that allows it to receive/create information; we are still left with the need for an Intelligent designer of of the “search algorithm”.

    • The answer is very simple yet perplexing:

      Organisms have agency.

      The way you use the autosuggest on your phone when texting illustrates this.

      Autosuggest is an algorithm. If you start using it and you ONLY choose the first choice it gives you, you’ll end up with gibberish. It’s not capable of constructing sensible sentences; it only produces statistical patterns.

      That is the limitation of an algorithm.

      But if you are able to always choose one of the three suggested words however you wish (but NEVER allowed to type anything), you can still usually say something intelligible and you could keep it going for quite a long time. And the result might be bad English… but it would be English nevertheless and it would make sense.

      That is what an algorithm is capable of when directed by an entity that possesses agency.

      All cells and all living things possess some degree of agency. This is the solution to the problem Marks presents in his book. I know him by the way and I agree with his book. His book is compatible with Third Way ideas. However he doesn’t so much emphasize that the agency comes from the organism itself. An entity with the ability to make free choices (=agency) can definitely create information, just as you are doing when you choose autosuggest options on your phone.

      My book Evolution 2.0 develops this idea further.

      • The obvious question then is “OK so where did all this genetic engineering capability come from?”

        An Intelligent Design (a la Discovery Institute) view would be that it was engineered by God.

        Another explanation might be that the universe is consciousness first, matter second and not the other way around. If the Evolution 2.0 Prize (see link at top of this site) can be won, then this is the likely explanation of how it can be won – by figuring out what consciousness is and where it comes from. At the present moment we have almost no answers to this question.

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