Four ways that the progress of experimental science conflicts with atheism

Apologetics and the progress of science
Apologetics and the progress of science

When people ask me whether the progress of science is more compatible with theism or atheism, I offer the following four basic pieces of scientific evidence that are more compatible with theism than atheism.

Here are the four pieces of evidence best explained by a Creator/Designer:

  1. the kalam argument from the origin of the universe
  2. the cosmic fine-tuning (habitability) argument
  3. the biological information in the first replicator (origin of life)
  4. the sudden origin of all of the different body plans in the fossil record (Cambrian explosion)

And I point to specific examples of recent discoveries that confirm those four arguments. Here are just a few of them:

  2. Examples of cosmic fine-tuning to allow the existence of conscious, embodied life (From the New Scientist)
  4. Evidence showing that Ediacaran fauna are not precursors to the Cambrian fossils, (from the journal Nature)

Atheists will typically reply to the recent scientific discoveries that overturned their speculations like this:

  4. Maybe we will find a seamless chain of fossils that explain how the Cambrian explosion occurred slowly, over a long period time

Ever heard any of these responses?

Below I list some resources to help you to respond to the four responses of atheists to the experimental data.




The impossibility of a bouncing universe





















Building blocks:

The oxidation state of Hadean magmas and implications for early Earth’s atmosphere

Dustin Trail, E. Bruce Watson & Nicholas D. Tailby



Functional protein sequences:


Estimating the prevalence of protein sequences adopting functional enzyme folds.

Axe DD.




So atheists are in double jeopardy here. They don’t have a way to build the Scrabble letters needed for life, and they don’t have a way to form the Scrabble letters into meaningful words and sentences. Point out that the more research we do, the tougher the problem gets to solve for naturalists, and the more it looks like an effect of intelligence. Write out the calculations for them.

4) The best candidate to explain the sudden origin of the Cambrian era fossils was the Ediacaran fauna, but those are now recognized as not being precursors to the Cambrian fossils.

Science Daily reports on a paper from the peer-reviewed journal Science:





The trend is that there is no evolutionary explanation for the body plans that emerged in the Cambrian era. If you want to make the claim that “evolution did it”, then you have to produce the data today. Not speculations about the future. The data we have today says no to naturalism. The only way to affirm naturalistic explanations for the evidence we have is by faith. But rational people know that we need to minimize our leaps of faith, and go with the simplest and most reasonable explanation – an intelligence is the best explanation responsible for rapid generation of biological information.


I do think it’s important for Christians to focus more on scientific apologetics and to focus their academic careers in scientific fields. So often I look at Christian blogs, and I see way too much G. K. Chesterton, Francis Chan and other untestable, ineffective jibber-jabber. We need to bring the hard science, and stop making excuses about not being able to understand it because it’s too hard. It’s not too hard. Everyone can understand Lee Strobel’s “The Case for a Creator“. That’s more than enough for the average Christian on science apologetics. We all have to do our best to learn what works. You don’t want to be anti-science and pro-speculation like atheists are. I recommend reading Uncommon Descent and Evolution News every day for a start.

20 thoughts on “Four ways that the progress of experimental science conflicts with atheism”

  1. That’s a slam dunk, WK – thanks – into my file! Now, on Chesterton, they can quote him AFTER all of the good science and apologetics – I do that with CS Lewis some. Makes a good combination.


  2. New Scientist link is no good:


    1. Please explain how the Universe was created and life started from non-life and how evolution has moved from 1 amino acid to what we see today and why there is not anywhere near enough fossils to show evolution and that every evolutionist has a different take on how to fill in all the gaps in this hypothesis of evolution. God Bless Raymond


      1. Life didn’t start from 1 amino acid, there are 22 essential amino acids that living things absolutely require. There are over 200 other known amino acids that are synthesized by living cells from the same basic chemical building blocks, but do not occur naturally and are not absolutely necessary to life.

        The current scientific inquiry into how life began has been focusing mainly on determining whether those 22 required amino acids can exist in nature without the pre-existence of life and how they might assemble into a self-replicating molecule. That is, if those 22 amino acids can be found in nature, then all the necessary chemicals for life already exist and the chemical interactions that could lead to life would be possible.

        So far, not only have the 22 amino acids been shown to have natural sources on Earth, but several of them have been shown to exist even on comets in space. Some amino acids are much more prevalent than others, occurring from very common chemical pathways in nature. Others are much less common and don’t have obvious pathways, however, experiments showed that those amino acids would form from the base chemicals if electricity was passed through a ‘soup’ of those chemicals. This was the basis of the ‘chemical soup’ hypothesis that put forth the idea that the early Earth would have had regions that contained the necessary base chemicals and lightning would provide the necessary electrical discharges. Thus showing that all the necessary amino acids could have existed on the early Earth.

        However, the chemical soup hypothesis, while intriguing, does not fully explain how all those amino acids could form a self-replicating molecule that could then evolve into a self-replicating organism like the cells we know today. There are many other ongoing studies to figure that out.

        Seeing as you don’t seem to have a good ability to research topics such as this I’ll list some basic searches you can put into Google to get more information.

        “what are amino acids”

        “how many amino acids are there” -> note the google says 20, but this is an outdated number that has not yet been corrected to say 22

        “miller-eury experiment”

        “amino acids found on comets”

        “amino acids role in evolution”

        Happy reading!


        1. Barius, the number would need to be 44, not 22. It would need to include both the left-handed and right-handed isomers of each of those amino acids.

          Then, one would have to explain how the undirected processes of random mutation and natural selection, resulting in only the left-handed isomers showing up in living systems. This characteristic is known as homochirality.

          For a simple 150 amino acid sequence like Doug Axe tested, just the probability of having a left-handed isomer at EVERY location would be (1/2)^150 or 7.e-46.

          So, just finding these amino acids in nature is necessary, but not sufficient. Homochirality is a puzzle, which still plagues evolutionary biology.


          1. The sequence is a puzzle, the chirality is a puzzle, the interfering cross-reactions are a puzzle, the radiation hazard problem, etc. etc. Everything is easy if you have naturalistic faith, though.


          2. That is a good analysis, and one which is fast approaching the limit of mathematical impossibility, about 1 in 10^80, the number of sub-atomic particles in the universe. One more reason that I just do not have enough faith (anymore) to be an atheist.


  3. Even if the data supports theism and that is somewhat debatable that doesn’t mean it supports monotheism or Christianity.


    1. A.B., that is almost a true statement. The scientific evidence supports either theism (which includes Christianity, Judaism and Islam) or deism.

      Pantheism (e.g., Hinduism) asserts that everything in the universe (matter & energy) collectively make up “god” (Atman is Brahman).

      Classical atheism held to the notion of eternal universe.

      If the universe had a beginning (and all the measurements to date seem to indicate that it did), then neither pantheism nor atheism are true. In the case of pantheism, Brahman (the supreme absolute) did not exist at one point. In the case of atheism, the universe is itself an effect and not the first cause.

      From science we can infer the First Cause had to be:
      – Powerful
      – Ancient (older than 13.75 billion years)
      – Non-material
      – Existing beyond 4-dimensions of space/time (we first started considering this in the use of tensors, 9-dimensional factors used to solve equations, such as Maxwell’s Equation and the Navier-Stokes Equation; later shown to be 10+ dimensions by Hawking in his string theory)
      – Intelligent (based upon the fine tuning we see in the universe and the complex information we see in living things)
      – Purposeful – design implies purpose.


      1. Thank you for posting that scientific refutation of pantheism. Very timely in another conversation I am having.


  4. Wintery Knight,

    Thanks for the interesting post! I have a question, though. Why did God wait so long to reveal this evidence? 99% of human history unfolded before these were discovered. Did God not care about revealing himself to these people? Why are we privileged?

    Further, even among people living today, 99% of us will probably never become familiar with this data. Why did God choose to make the evidence for his existence so inaccessible?

    Consider this analogy. Imagine woman who gives up her child from adoption. If she wants her child to know about her existence, it would be extremely bizarre for her to reveal her existence to her child in a latter written in Egyptians hyrogliphics and bury it in the cement that holds together the fireplace in the child’s new house. It is unlikely that the child would ever find the letter, let alone understand it. Why would a woman who wants her son to know her make the evidence for her existence so hard to find and understand? Why would God?


    1. Hey Ron, great questions!

      The 99% of history issue is a pretty easy question, since 98% of people who have ever lived have lived since Christ. So, it’s not the years, but the population who can access the Light.

      God is not constrained by time and resources like we engineers are. As for why 99% of us do not have direct access to the high-end technical data, God has promised that those who respond to His general revelation with sincere truth-seeking hearts WILL be provided any additional information about Him that is necessary for salvation. That does not even necessarily include the high-end evidence. Any person can look up into the night skies and have an appreciation for the Contingency Argument for the Existence of God – in a non-formal sense. (In my case, however, as a former atheist for 42 years, God DID need to lead me through the high-end philosophy and science, in an evidential sense. I would NEVER have believed otherwise, and He knew that. He gives us what we specifically need.)

      This is just a rough order reply, Ron – please excuse me for not providing the good philosophical links and citations to this, as well as any Bible verses you might want to see that corroborate with same. If you reply to this with more questions, I promise to give a richer reply when I am not under the gun timewise – those are great questions and I sincerely appreciate them and the intellectual thought that you put into them!


    2. To answer your question directly would require knowledge of God’s plan that I don’t have. So the answer is “I don’t know”.

      But I do have three responses.

      The first would be for you to read something about middle knowledge, to find out how God can place people in the right time and place so that they will get the level of evidence they need respond to him, if they are able to.

      Second, some people get lots of evidence of God, and they don’t respond, so it’s not as simple as just giving all the evidence to everyone, since God expects more than just head knowledge, he expects pursuit, responsiveness, engagement.

      Third, I think that God is revealing more scientific evidence now because people have a harder time believing in God as they become more and more focus on sexual pleasure and materialism.


  5. Multiverses are a theory that some physicists invoke in order to avoid conclusions that (1) they personally dislike and (2) would otherwise be forced to accept about the one universe that we *can* observe and test.

    PS: Even the existence of the multiverse theory should serve as an indicator to the seriousness of the problems confronting those who seek purely naturalistic explanations that align with all presently available experimental data. Not to say such an explanation is impossible — but they will have to do much better than multiverses.

    PPS: I like the observation that invoking multiverses requires faith.


  6. There are other mysteries in microbiology that plague evolutionary biology. I will just briefly mention them here:

    – The property of homochirality: how living organisms use only protein sequences made up of left-handed isomer amino acids in every location.

    – The growing number Open Reading Frame (ORFan) genes being discovered by the ENCODE project, which have no homology.

    – Distributed gene regulatory networks (dGRNs), scaffolding for regulating genes and transmitting proteins. These networks have been found to follow a power law with respect to their robustness ( By contrast, random networks typically follow a Poisson distribution.

    – How cells differentiate from undifferentiated stem cells into unique tissue types. Every cell in our body contains the same DNA (with all the genes). During cell differentiation, different epigenetic markers activate certain genes and silence others, for each tissue type. (There over 200 different tissue types in the human body.) These markers are maintained through countless generations of cell mitosis for the life of the organism. So, while you have one genome, you have over 200 different epigenomes. Scientists do not understand what triggers and controls these markers.

    – Your body plan is not stored in your DNA. Scientists have yet to find it. Perhaps that is passed down epigenetically from parent to offspring, which might explain why there is limited descent with modification. This would fit well with the fossil data, which shows a forest of bushes instead of a single “tree of life” postulated by Darwin.

    – There at least four separate codes seen within cells (there may be more):

    — DNA. In humans this is a 4-symbol, error correcting code which is over 3.1 billion base pairs in length. The areal density of DNA is so compact, that 4 grams of mitochondrial DNA (which stays intact for thousands of years), could store the world’s consumption of data (presently just over 2 zettabytes).

    — tRNA – there are 3 codons per amino acid site, allowing for 4^3 or 64 possible combinations. Only 22 left-handed isomer amino acids are selected. The first two codons are non-synonomous, meaning they greatly influence amino acid selection.

    — The 3rd codons are synonomous, meaning they don’t greatly influence the selection of the amino acid at each location. However, studies at the University of Washington indicate that the sequence of the 3rd codons (referred to as duons), make up a code which is related to the regulation of the protein or enzyme created.

    — Histone codes: Your DNA strands are wrapped around bundles of 8 histone proteins, resembling a string of pearls. When the strands are open, this is indicative of active gene sites. When the genes are silenced, these sites become highly packed and serve as part of the chromatin structure. There are over 50 histone combinations. Some believe it is another “code”.

    Our uniform and repeated experience is that information this complex, which provides meaning or function, comes from only one source: creative intelligence.


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