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:

  1. An explanation of 3 of the 6 experimental evidences for the Big Bang cosmology (From an article from Caltech)
  2. Examples of cosmic fine-tuning to allow the existence of conscious, embodied life (From the New Scientist)
  3. Evidence that functional protein sequences are beyond the reach of chance, (from Doug Axe’s JMB article)
  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:

  1. Maybe the Big Bang cosmology will be overturned by the Big Crunch/Bounce so that the universe is eternal and has no cause
  2. Maybe there is a multiverse: an infinite number of unobservable, untestable universes which makes our finely-tuned one more probable
  3. Maybe the origin of life could be the result of chance and natural processes
  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.

1) The Big Crunch/Bounce has been disproved theoretically and experimentally.


Nature 302, 505 – 506 (07 April 1983); doi:10.1038/302505a0

The impossibility of a bouncing universe


*Center for Theoretical Physics, Laboratory for Nuclear Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

†Department of Physics, University of California, Irvine, California 92717, USA

Petrosian1 has recently discussed the possibility that the restoration of symmetry at grand unification in a closed contracting Robertson–Walker universe could slow down and halt the contraction, causing the universe to bounce. He then went on to discuss the possibility that our universe has undergone a series of such bounces. We disagree with this analysis. One of us (M.S.) has already shown2 that if a contracting universe is dominated by radiation, then a bounce is impossible. We will show here two further results: (1) entropy considerations imply that the quantity S (defined in ref. 1 and below), which must decrease by ~1075 to allow the present Universe to bounce, can in fact decrease by no more than a factor of ~2; (2) if the true vacuum state has zero energy density, then a universe which is contracting in its low temperature phase can never complete a phase transition soon enough to cause a bounce.


The universe is not only expanding, but that expansion appears to be speeding up. And as if that discovery alone weren’t strange enough, it implies that most of the energy in the cosmos is contained in empty space — a concept that Albert Einstein considered but discarded as his “biggest blunder.” The new findings have been recognized as 1998’s top scientific breakthrough by Science magazine.

[…]The flood of findings about the universe’s expansion rate is the result of about 10 years of study, said Saul Perlmutter, team leader of the Supernova Cosmology Project at Lawrence Berkeley National Laboratory.

Perlmutter and others found such a yardstick in a particular kind of exploding star known as a Type 1A supernova. Over the course of several years, the astronomers developed a model to predict how bright such a supernova would appear at any given distance. Astronomers recorded dozens of Type 1A supernovae and anxiously matched them up with redshifts to find out how much the universe’s expansion was slowing down.

To their surprise, the redshift readings indicated that the expansion rate for distant supernovae was lower than the expansion rate for closer supernovae, Perlmutter said. On the largest scale imaginable, the universe’s galaxies appear to be flying away from each other faster and faster as time goes on.

“What we have found is that there is a ‘dark force’ that permeates the universe and that has overcome the force of gravity,” said Nicholas Suntzeff of the Cerro Tololo Inter-American Observatory, who is the co-founder of another group called the High-z Supernova Search Team. “This result is so strange and unexpected that it perhaps is only believable because two independent international groups have found the same effect in their data.”

There has only been one creation of the universe, and the universe will never reverse its expansion, so that it could oscillate eternally. That view is popular, perhaps in part because many people watched videos of Carl Sagan speculating about it in public school classrooms, but all it was was idle naturalistic speculation, (Sagan was a naturalist, and held out hope that science would vindicate naturalism), and has been contradicted by good experimental science. You should be familiar with the 3 evidences for the Big Bang (redshift, light element abundances (helium/hydrogen) and the cosmic microwave background radiation. There are others, (radioactive element abundances, second law of thermodynamics, stellar lifecycle), but those are the big three. Point out how the experimental evidence for the Big Bang has piled up, making the problem even worse for the eternal-universe naturalists.

2) The multiverse has not been tested experimentally, it’s pure speculation.


Multiverse thinking or the belief in the existence of parallel universes is more philosophy or science fiction than science. ”Cosmology must seem odd to scientists in other fields”.

George Ellis, a well-known mathematician and cosmologist, who for instance has written a book with Stephen Hawking, is sceptical of the idea that our universe is just another universe among many others.

A few weeks ago, Ellis, professor emeritus of applied mathematics at the University of Cape Town, reviewed Brian Greene’s book The Hidden Reality: Parallel Universes and the Deep Laws of the Cosmos (Knopf/Allen Lane, 2011) in the journal Nature. He is not at all convinced that the multiverse hypothesis is credible: ”Greene is not presenting aspects of a known reality; he is telling of unproven theoretical possibilities.”

According to professor Ellis, there is no evidence of multiverses, they cannot be tested and they are not science.

Ellis is not the only multiverse sceptic in this universe. A few months ago, science writer John Horgan wrote a column in Scientific American, expressing his doubt in multiverses.

When you get into a debate, you must never ever let the other side get away with asserting something they have no evidence for. Call them on it – point out that they have no evidence, and then hammer them with evidence for your point. Pile up cases of fine-tuning on top of each other and continuously point out that they have no experimental evidence for their speculations. Point out that more evidence we get, the more cases of fine-tuning we find, and the tougher the problem gets for naturalists. There is no evidence for a multiverse, but there is evidence for fine-tuning. TONS OF IT.

3) Naturalistic theories for the origin of life have two problems: can’t make the amino acids in an oxydized atmosphere and can’t make protein and DNA sequences by chance in the time available.

Building blocks:

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

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

Nature 480, 79–82 (01 December 2011) doi:10.1038/nature10655

[…]These results suggest that outgassing of Earth’s interior later than ~200?Myr into the history of Solar System formation would not have resulted in a reducing atmosphere.

Functional protein sequences:

J Mol Biol. 2004 Aug 27;341(5):1295-315.

Estimating the prevalence of protein sequences adopting functional enzyme folds.

Axe DD.

The Babraham Institute, Structural Biology Unit, Babraham Research Campus, Cambridge CB2 4AT, UK.

Proteins employ a wide variety of folds to perform their biological functions. How are these folds first acquired? An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional folds.

[…]Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.

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:

Evidence of the single-celled ancestors of animals, dating from the interval in Earth’s history just before multicellular animals appeared, has been discovered in 570 million-year-old rocks from South China by researchers from the University of Bristol, the Swedish Museum of Natural History, the Paul Scherrer Institut and the Chinese Academy of Geological Sciences.

[…]This X-ray microscopy revealed that the fossils had features that multicellular embryos do not, and this led the researchers to the conclusion that the fossils were neither animals nor embryos but rather the reproductive spore bodies of single-celled ancestors of animals.

Professor Philip Donoghue said: “We were very surprised by our results — we’ve been convinced for so long that these fossils represented the embryos of the earliest animals — much of what has been written about the fossils for the last ten years is flat wrong. Our colleagues are not going to like the result.”

Professor Stefan Bengtson said: “These fossils force us to rethink our ideas of how animals learned to make large bodies out of cells.”

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:
    Examples of cosmic fine-tuning to allow the existence of conscious, embodied life (From the New Scientist)

    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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