Darwinists Underestimate Nature. Creationists Underestimate God.

Doug Brewer poses a fantastic question:

Chloroplasts are actually blue-green algae living symbiotically inside plant cells. They have their own DNA and represent the most successful merger-acquisition in the history of earth.

Chloroplasts are actually blue-green algae living symbiotically inside plant cells. They have their own DNA and represent the most successful merger-acquisition in the history of earth.

You say that “We can produce new species at will and it happens all the time”.

Do you believe that these same processes which create (what you refer to as) “new species” are also capable of creating new genera, families, orders, classes, phyla and kingdoms?

If so, how?

If not, all you have done is make a slight adjustment to the position (or to the name) of the line which marks the limits of biological change, but the very real limits remain.

If so, we still come back to some form of Intelligent Design as the only other explanation for the origin of new genera, families, orders, classes, phyla and kingdoms.

Doug, allow me to relay a story from Evolution 2.0, Chapter 24, titled “Beyond “God of the Gaps”: A New Paradigm for Biology.” I quote Stephen Hawking from his book God Created the Integers.

One of Isaac Newton’s supporters asked the great scientist, “Could the solar system, with the planets all revolving around the sun in the same direction in almost the same plane, be formed out of an initial uniform distribution of matter by the action of only natural causes, or was it evidence of design?” (218).

Newton answered that his system could in no way explain these obvious regularities in the heavens, that they could not result from the action of only natural causes. The cause “had to be not blind and fortuitous, but very skilled in Mechanics and Geometry.”

Hawking continues:

And so matters stood for nearly the entire eighteenth century until mathematician Pierre Simon de Laplace blazed his way across the firmament of French science. In 1770, Laplace began a rapid outpouring of papers on a wide variety of topics in pure and applied mathematics, drawing wide attention to himself.

The most important papers focused on outstanding problems in planetary theory. The orbits of the two largest planets Jupiter and Saturn sometimes lagged behind and sometimes ran ahead of their predicted position. Laplace sought to explain how the planets influenced each other in their orbits.

This is a more difficult problem than the three-body problem which even today can only be solved by successive approximations. Laplace demonstrated that perturbations were not cumulative, as Newton feared, but periodic. God did not need to intervene to keep the Solar System from collapsing. (218)

Doug, here’s what we know: Two processes produce new species in real time –

1) Hybrids, where Species 1 crossed with Species 2 gives you Species 3. Example: Emmer wheats + goat grass = modern wheat.

This doubles the number of chromosomes. After this merger, “hybrid dysgenesis” kicks in. Extensive genome editing re-arranges and deletes parts of the new DNA.

Genome studies indicate that a hybridization event of this kind got us from invertebrates to vertebrates. Then a second one got us from vertebrates to jawed vertebrates. This is called “Ohno’s 2R hypothesis,” where the “2R” stands for “2 Rounds of doubling” of chromosomes.

2) Symbiotic events where cells merge. Quoting from Evolution 2.0:

Dr. Kwang Jeon, a professor at the University of Tennessee, did an experiment where tens of thousands of bacteria took up residence inside Amoeba proteus organisms. A fierce parasitic attack ensued, killing almost all the amoeba.

But in the space of a year, amoeba and bacteria entered into symbiosis. Both modified expression of their genes as necessary, to support the mutual dependence (624, 636, 653, 652).

Jeon learned how to reliably trigger symbiotic cell mergers between amoeba and bacteria. It took 200 generations, about 18 months, for the cells to become fully interdependent. After that, removal of either symbiotic partner proved fatal to both (625).

We have excellent reasons to believe a similar symbiotic merger was responsible for plant cells (eukaryote + blue-green algae = plant cell with chloroplast).

Likewise, mitochondria are symbiotic bacteria living inside animal cells. Both mitochondria and chloroplasts have their own DNA.

In other words every green leaf and blade of grass you’ve ever seen is green because blue-green algae lives symbiotically inside plants.

Your ability to use oxygen comes from symbiotic bacteria.

The whole biology good ol’ boys club thought Lynn Margulis was crazy when she introduced this idea to the West in the 1960s. But the Russians had already figured it out 50 years before.

Now add…

  • Horizontal Gene Transfer, cells exchanging DNA;
  • Transposition: re-arrangements of DNA in response to changes in the environment
  • Epigenetics, heritable switching of genes on and off in response to environment
  • Retroviruses, which play a major role transferring genetic material from anywhere to almost anywhere else
  • Protozoans can splice their DNA into 100,00 pieces and re-arrange them in real time, in response to threats. This is almost unfathomably sophisticated, but it’s a fact.

…and collectively you get a “Swiss Army Knife” of genetic tools that are, in principle, capable of getting you anywhere on the tree of life to anywhere else.

Darwinists have this naive conception that random copying errors with natural selection have godlike powers and can do anything.

Of course this violates every principle of information theory and probability known to man; this is why Darwinists scream bloody murder any time someone brings up statistics. But it’s impossible for accidental processes to do this. They may as well believe in Superman or the Easter Bunny.

ID people and creationists acknowledge the extreme difficulty of these processes. They believe divine intervention is necessary. But I say nature has enough ingenuity to do this. She is endowed with enough power to pull this off.

Such processes can be studied and reproduced. We can come to understand them better.

#Evolution in 140 characters or less: Genes switch on, switch off, rearrange and exchange. Hybrids double; viruses hijack; cells merge; winners emerge.

This is not the ID position.

ID (as understood by the general public) is exactly what you appear to believe: That “real limits remain” and divine intervention is necessary.

I say nature’s Swiss Army Knife is capable of generating life’s diversity. Mother nature is vastly more amazing than people give her credit for.

I recommend you read my book and James Shapiro’s book Evolution: A View from the 21st Century cover to cover. If my view is only just another form of ID… then why don’t the ID books tell you this stuff?

And… why is this third way view important and valuable? Because it does not pit theology against science. This is a view which stands a chance of being accepted in the academy.

ID as currently understood by most people will never be accepted by the mainstream.

Darwinists underestimate nature. Creationists underestimate God.

Download The First 3 Chapters of Evolution 2.0 For Free, Here – https://evo2.org/evolution/

Where Did Life And The Genetic Code Come From? Can The Answer Build Superior AI? The #1 Mystery In Science Now Has A $10 Million Prize. Learn More About It, Here – https://www.herox.com/evolution2.0

46 Responses

  1. Jonathan Vlietstra says:

    Very interesting, I was not aware my knowledge of evolution and genes was that shallow. But it enforces what I knew, that nature has the tools for evolution.

  2. Jim O'Hara says:

    Bingo. Well written. Nature Is liquid and transforms as needed.

  3. Jim Munro says:

    So who designed and manufactured your ‘Swiss Army Knife’?
    The ‘simplest’ living cell requires numerous complex and interdependent components, all of which would need to be precisely assembled together in an instant of time to avoid destructive natural processes (if you assume the improbable possibility that any one of those complex components could form from random chemical processes?)
    You seem to infer that the atoms and molecules of the universe have some kind of innate intelligence? You ‘worship’ that which is created, and refuse to acknowledge the Creator GOD who has revealed Himself throughout human history. Don’t play games with your eternal destiny!

    • I don’t think you know what my position is. Read more of the site, please.

    • Rodrick says:

      Well said….Exactly right..

    • Fred Griffith says:

      Jim, you appear to suggest that the author of this article believes that atoms and molecules have innate intelligence. You also suggest that the author worships the universe, a created thing, instead of the creator. It is my understanding that God is believed to be omnipotent, omnipresent, eternal, and infinite. After all who would want to worship anything less then the supreme totality of divinity?

      Of course, if God is infinite, God must contain all parts of the universe. All stars and planets, interstellar dust, moons, asteroids, and everything upon those bodies, living or nonliving. This includes the Atoms and molecules that you disparage.

      God’s intelligence, is contained within and without the physical parts of the universe and any other planes of reality which might exist. There is no other place it could be if God is infinite. If, indeed, the author does worship the creation, rather than the creator, what does it matter if he were to worship that part of the Divine that has manifest in the physical universe?

      While such a person does not worship the God in which you believe, it could be only because that person recognizes the Divinity inherent to all things and people, instead of bowing down to a God of a small tribe of humans; who claims to be infinite yet also claims to to be separate from the people and places who have physically manifested within itself.

      While Gods which resemble humans are a simple way to understand part of the Divine, these are myths which actually represent only part of the infinite God, not the totality. To think that the version of God in which one believes is truth, much less the only truth, is extreme hubris. End of rant.

    • Phuzzy says:

      Maybe the elements DO have innate intelligence.

    • That’s an Origins or Bust argument. But the reptile-mammal transition (RMT), as just one example, doesn’t go away (or become less natural or inexplicable) based on how the first replicators originated 3 billion years earlier. The RMT shows all the hallmarks of microevolutionary processes resulting in a macroevolutionary outcome over a hundred million years, and as I covered in “Evolution Slam Dunk” book, paleogenomics is advancing to retroengineering the steps in such changes, from the dynamics generating mammal tooth form to how rib evolution occurred. Since all this work is being done by “Darwinists” it is hardly the case that they are underestimating anything about Nature, as they are doing the work to figure out what actually happened, and so revealing all the fine evolutionary details at every turn.

  4. Jim Golding says:

    Your debate with PZ seemed inconclusive however he was clearly threatened and went ad hominem on you. As a layman I still find DNA repair as random dubious, so with what I was able to understand I would say you prevailed.

  5. Jim Golding says:

    I found your debate with PZ compelling. Kudos.

  6. Jim Golding says:

    http://www.ncbi.nlm.nih.gov/books/NBK6360/ could you comment on this? Is this a prize winner or simply a description of early development?

  7. Don Smith says:

    How does this article fit into your studies?
    Bacteria are more capable of complex decision-making than thought:

  8. Don Smith says:

    Your article said:
    Now add…
    Horizontal Gene Transfer, cells exchanging DNA;
    Transposition: re-arrangements of DNA in response to changes in the environment.
    These are functions, actions performed by living systems. What is the lowest common denominator for these functions, before they can’t be reduced any further?

    • We are a LONG way from knowing the answer to that question. Centuries, maybe.

      • Ken Meyer says:

        Actually, we are at the beginning of this very understtanding. In a 4200 word piece of writing, I identify the understanding. Now, the only task is that I am just, to the world at large, another bubble of soap suds from which to choose!

    • The lowest common denominator is nutrient-dependent RNA-mediated DNA repair. In the context of the physiology of reproduction, it links atoms to ecosystems via the innate immune system. Fixed amino acid substitutions stabilize all organized genomes.

      See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems. https://dx.doi.org/10.6084/m9.figshare.994281

      Now see: “Team uses internet network theory to decipher the first epigenetic communication network” January 28, 2016 http://phys.org/news/2016-01-team-internet-network-theory-decipher.html

      They are reporting what I detailed in an invited review of nutritional epigenetics. But they place it into the context of nutrient-dependent epigenomic co-localization and co-evolution. They don’t seem to realize the communication hub in the chromatin network of embryonic stem cells does not automagically evolve.

  9. Re: “Laplace demonstrated that perturbations were not cumulative…”

    I’m interested in attempts to apply mathematical models to biologically-based cause and effect. For example, the misrepresentations include this one: Human brain networks function in connectome-specific harmonic waves http://dx.doi.org/10.1038/ncomms10340

    Excerpt: We found that structured oscillatory patterns naturally self-organize on the human connectome for a wide-range of diffusion parameters in the model (Fig. 4a–d; Supplementary Figs 8 and 9; Supplementary Movies 1–4).

    Theorists willingly extend “…a universal mathematical framework, eigendecomposition of the Laplacian, to the anatomical structure of the human connectome…” without the energy-dependent organization of cells and RNA-mediated cell type differentiation.

    That’s why theorists are the subjects of parodies like this one. It links atoms to ecosystems by what is known to serious scientists about energy-dependent changes in base pairs.


  10. Plants with biosensors may light the way http://news.harvard.edu/gazette/story/2016/02/plants-with-biosensors-may-light-the-way/

    The technology they introduce shows how “…ordinary organisms can be transformed into extraordinary living cellular devices that can sense specific signals and produce appropriate responses…”

    All living genera must sense, signal, and respond appropriately. The sensing, signaling and responding begin involve RNA-mediated amino acid substitutions. That fact was the subject of my reviews in 2012 and 2013.

    http://www.ncbi.nlm.nih.gov/pubmed/24693349 2012 Excerpt: “Philosophically and metaphorically, these neural networks extend to mammalian brains. The concept that is extended is the epigenetic tweaking of immense gene networks in ‘superorganisms’ (Lockett, Kucharski, & Maleszka, 2012) that ‘solve problems through the exchange and the selective cancellation and modification of signals (Bear, 2004, p. 330)’. It is now clearer how an environmental drive probably evolved from that of food ingestion in unicellular organisms to that of socialization in insects.”

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960065/ 2013 Excerpt: “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it. (Max Planck, 1858–1947)”

  11. Lee says:

    Most of the creationists I have encountered do not “underestimate God,” they are simply convinced that evolution is a lie made up by atheists to claim that God does not exist. They don’t care what God can and cannot do. They only care that anyone who does not deny evolution is trying to disprove the existence of God.

    “You say God created evolution? YOU ARE DENYING THE EXISTENCE OF GOD!!!!!!!!!!!!!!!!!!!!!!”

    How can you argue with such a person? How can you educate such a person, armed as he is with the full armor of God, including the shield of faith that you are of Satan, and confidence that the sword of Biblical citations will cut you to pieces (have already….)?

    Good luck.

  12. Dave says:

    Hello Perry.

    Outstanding job. I’ve been following your work for years. Thx.

    Can you provide very brief answers to your beliefs on these?

    Q: Is this the only universe?
    Q: Were there a historical first two humans (“Adam and Eve”) that gave us our entire species or were more contributors to our species?
    Q: Does DNA show that there were other human species that existed and the one we have today is simply the simply didn’t die out?
    Q: Do humans have a unique dimension apart of from the animals (e.g. having supernatural spirit, not just a natural soul)
    Q: Did the first human sin produce an event called “the Fall”?
    Q: Was the Fall an event or a process?
    Q: Did the Fall produce a spiritual death or physical death, both, or neither?
    Q: If the Fall produced either spiritual or physical death, did either of these occur before the Fall?
    Q: Did the Fall result in corruption that affected the rest of the cosmos?

    Cheers, Dave

    • Deandra says:

      Just to clarify, I have only witnessed women attending EQ a handful of times. This is excluding setting apart a new EQ pryiedsnce. I am not sure why they were there. Generally they were visitors that I did not know.My wife tells me that members of the bishopric attend RS somewhat regularly.

    • Perry has his own response, but here are my replies on those questions:

      Q: Is this the only universe? Maybe not, there is evidence (certain cosmological cold spots) that are implied by extradimensional universes interacting). The Bible & other religious traditions are not particularly informative on this issue.

      Q: Were there a historical first two humans (“Adam and Eve”) that gave us our entire species or were more contributors to our species? No on both. The human species (and by extension all the way back into the hominids and beyond) are populations, the Adam & Eve story is just that, a pleasant narrative fiction coming from a pre-scientific age.

      Q: Does DNA show that there were other human species that existed and the one we have today is simply the simply didn’t die out? Yes, if by “human species” you mean within genus Homo. Neanderthal and Dmanisi are rare instances of where the cousins are young enough to extract DNA to compare, but the existence of other species within our genus has a plethora of fossils available on that, regardless of the DNA side. The Neanderthal case has reached the “how much interbreeding did we do” stage (a few hundred matings in the Middle East, with results cascading through Eurasian genome).

      Q: Do humans have a unique dimension apart of from the animals (e.g. having supernatural spirit, not just a natural soul). Apparently not. The whole idea of an extraphysical soul is on shaky grounds neurobiologically (how can we ever be “unconscious” for example). Our distinctive feature is likely not our self-awareness (animals have degrees of that which can be discerned in studies) but that we have a grammatical language system that allows us to make up stories about what we believe to be true, and things we want to be true. The research there is just beginning to pin down the mechanisms, but those hoping for some Maginot Line to emerge to insulate that from a natural origin, well, don’t bet the house on that.

      Q: Did the first human sin produce an event called “the Fall”? That is a theological claim from the aforementioned Bible story, contingent on the Adam & Eve thing. No need to think any of that happened at all, so the sin/Fall cascade is purely driven by how much believers want that part of the story to be true.

      Q: Was the Fall an event or a process? It was a non-event, so neither.

      Q: Did the Fall produce a spiritual death or physical death, both, or neither? See above.

      Q: If the Fall produced either spiritual or physical death, did either of these occur before the Fall? See above.

      Q: Did the Fall result in corruption that affected the rest of the cosmos? See above.

      It is true that Young Earth Creationists are more explicitly comfortable with taking the Fall whole hog, but then they take the whole story that way, which is why watching religious apologetics on this front can be of great amusement, seeing which aspects of the natural world and history have to be overlooked or tweeked.

      The available history suggests religions developed slowly in humans, but that the version found in the Bible story only arrived long millennia down that road. It’s unlikely anyone rafting to Australia 40,000 years ago, or throwing up stones in Catal Huluk 9000 years ago, or marveling at the sun and moon’s patterns at Stonehenge more recently, had any Biblical Fall myths on their mind. Don’t forget in one’s parochial myopia that 40% of the planet don’t have belief systems that even bump into that Bible Fall story (2.6 billion Christians + 1.6 billion Muslims still leaves 2.8 billion outside that box). And tossing in the long 200,000 history of our species means most of the time people have not been believing any of that Bible story at all.

  13. Like many others, you seem to be confused about what can happen in the lab compared to what does not happen outside the lab.

    For example: Re: “1) Hybrids, where Species 1 crossed with Species 2 gives you Species 3. ”

    For comparison: Species of Drosophila http://www.sciencemag.org/content/177/4050/664.short
    Excerpt: “Hybrids of Drosophila pseudoobscutra and D. persirnilis are easily obtainable in the laboratory, but they are absent in localities where both species occur side by side (14).”

  14. Fred Frederickson says:

    Just a lightning rod click bait story. Nothing more.

  15. Dave says:

    Hey Perry. Thx for the excellent work.

    Relevant to your book Evolution 2.0, can you review (at your convenience) William Lane Craig’s comments on these two podcasts. I think you will find him and QA portion generally pointing toward your materials, but I’d be curious where you disagree with these– thx! No rush. It’s very interesting where this is all headed.

    Blessings — Dave

    At your convenience,



    • I’m awfully pressed for time. can you give me some minute:second markers to facilitate?

      • Dave says:

        Thx Perry. I’ll try to find the key points and send, but I’d recommend putting these links in your bookmark list for a commute sometime. There’s a lot covered that’s relevant in both the lecture and QA.

        By the way, here are audio-only MP3 versions that have been post-processed to remove the silence breaks, even volumes and slightly speed the sound. I’ll leave them on my server for December. If you’re interested in these, please download. The total time for both talks is just 45mins. Cheers — Dave




        • Dave says:

          Thx Perry.

          I guess I’ll boil down to the two youtube videos in the previous post to this one question: What are the two best elevator pitches for and against common ancestry? One tree for all of life or many?
          Here’s my cut:

          One tree (from Dennis Venema):
          1. Genetic similarity with organisms overly redundant.
          2. Related kinds have the same ordering or sequence of genes.
          3. Broken DNA shared in similar organisms.

          Many trees:
          1. Transitional fossils widely missing
          2. Distances between life too far (e.g., sponge and whale)
          3. Mechanism doesn’t work; e.g, random produces entropy.

          Your solution in your book Evolution 2.0, explains a lot of the last three, but do you believe in one common tree or many and if so why?

          Based on my own experience of miracles, I think we can’t rule out many trees; though it does seem ad hoc.

          They argue both sides in those youtube videos (and the shorter MP3s I’ve listed above).

          Blessings! No rush. Have a good Christmas.


          • The best arguments AGAINST common ancestry are:

            1) To be honest I feel we have no more than 3-5% of the evolutionary picture solved. Neo-Darwinists imagine that Darwin solved everything 150 years ago with Natural Selection and everything since then is just cleanup. Not so. We have only the sketchiest understanding of adaptational processes. We have broad outlines of some things and exquisite details of other things, but the larger picture is quite messy.

            2) We don’t really know how an arm or wing or eye evolves; we only have bits and pieces of experimental evidence and the rest is anecdotal.

            3) “Orphan” or “ORFan” genes are often cited as evidence against common descent but we know for example that some bacteria can produce a different DNA mutation in *every single daughter bacterium* that divides off, producing millions of unique mutants. We know that cells are linguistic.

            If a person looks at all this and says “Well I just don’t buy common descent” my response is “Well you should at least look very hard for ways to make it work because it makes science and biology MUCH MUCH MUCH more elegant if it’s true and it’s a very impressive engineering achievement. It gives us much to learn from technologically.”

            I find that people who reject various theories ie common descent always ask questions other people don’t ask. They don’t always stick around for the answer but I’ve found that people from ALL perspectives in this debate say very useful things sometimes. Dissenters have different assumptions and those assumptions bring insights.

            So I welcome diversity and disagreement. As long as people bring facts to the table and not merely biases.

            The arguments FOR common descent are more anecdotal than direct, and are most strongly supported by a desire for parsimony. Hardly anybody seems to think that God placing a moon 250,000 miles from earth and then giving it a push is more elegant than it all coming from a single original big bang event.

            Certainly we can say that 20% of genes are found in 80% of all organisms; there is a great deal of commonality to all living things.

            For these reasons I advocate one tree rather than many.

            If someone wants to argue for many trees, I think they need to defend where they draw the lines of separation. I don’t see that as being any easier than drawing lines of connection. How many separate trees are there? I bet you’d have a hard time finding consensus on that one.

            • Scott Harwell says:


              from a cursory review your blogs and websites, it is abundantly clear that your atheist. From what I can also tell, you also ascribe to the truth of the Judeo-Christian religion.

              As for your theory of common descent, God certainly could have used this mechanism. Based on my cursory review of your posts, and the honest opinion that you devalue God’s word when it comes to creation and you are focusing on the similarities of DNA to point to common descent rather than a common designer.

              I am not a scientist and not even an engineer. However, as an attorney, I can see when someone takes inconsistent positions and this is what your theistic evolutionary view does when comparing it to Scripture.

              From my own research, and this is admittedly looking and reviewing the research through the lens of an attorney, seems to me that scientists like Shapiro are on the right track when it comes to evolution within certain designs created by God. This is the fundamental premise in Stephen Meyer’s book, “Darwin Doubt” and there is simply no evidence at this time that a simple cell could ever evolve into a more complicated living organism or into an entirely new type of creature or animal. Rather, based on my admittedly limited understanding, it seems to me that God created and designed DNA Pacific types of life forms which could adapt and “re-wire” its DNA and very short time frames in order to survive and adjust to changing conditions in the environment. This quick-adaptation of life has been used by macro evolutionists in years past to lob grenades at creationists when they would argue that there is no possible way number of species currently on the earth could have ever evolve and are descended from the “two of each kind” that were brought into and then emerged from Noah’s Ark. What current research has revealed, as it is moved away from the Darwinist view of natural selection and mutation, is that life did and can evolve in very brief periods of time.

              • Scott,

                Have you read my book?

                • Scott Harwell says:

                  Not yet. I may probably do so but from your websites and posts, it seems that you are a theistic evolutionist and believe in common descent. From all of the books I have read and studied on this topic, theistic evolution seems highly unlikely. My analogy would be a “simple” word processing program from the 1970’s not being able to evolve in to the current version of Word.

                  I do see evidence of “fast” microevolution and believe God “programmed” the DNA of life to quickly adapt to changing environments.

  16. Dave Nevins says:

    Hey Perry. Great work again.

    Do you have any thoughts on this new report indicating virtually all current animal species only date back 100,000 to 200,000 years?


    Also, if you haven’t already, I recommend you do a layman’s simplified Evolution 2.0 two-minute summary on YouTube that will generate buzz. It should be an concise distinction between old mindset vs. new evidence. That could really be great. Something anyone could get immediately, like a provacative, convincing elevator pitch. My two cents,

    with pics to distinguish: “we used to think it’s like this, but it’s really like this” E.g., we thought the sun rotated around the earth; but really the earth rotates around the sun — and they are both moving out from the galaxy center…”

    Cheers –Dave

Leave a Reply

You must use your real first and last name. Anonymity is not allowed.
Your email address will not be published.
Required fields are marked *