1.2 Modern Science vs Evolution

DNA, The Building Block of Life

In 1953, the double-helix structure of DNA was described. DNA stores the information cells use to build proteins and copy themselves. If human DNA were typed as letters (A, C, T, G), the ~3 billion letters would fill thousands of pages.

Key facts about DNA:

• DNA contains functional coding regions (genes). The human genome has roughly 20,000 protein-coding genes.
• Any two humans share ~99.9% of their DNA. The 0.1% difference accounts for variation in body shape, eye color, height, and so on.
• To create a new type of cell, you need new proteins, which require new functional DNA sequences. Estimates of how often random mutation could stumble onto a functional protein fold are extremely low, Douglas Axe’s experimental work (Journal of Molecular Biology, 2004) estimated roughly 1 in 10⁷⁷ for a modest 150-amino-acid protein. Even more generous estimates leave unguided chance with a very hard problem to solve in the time available.

Epigenetics

Environmental factors can change how genes are switched on or off. Epigenetics can regulate existing information, but it does not by itself write entirely new genetic code.

According to the National Human Genome Research Institute (NHGRI), the epigenome is made up of chemical tags and proteins that attach to DNA and direct actions such as turning genes on or off without changing the underlying DNA sequence; the same genome is interpreted differently in specialized cells (for example, muscle versus nerve). Those marks are often inherited when a cell divides, and factors such as diet, smoking, or infection can contribute to epigenomic change over a lifetime—still by reprogramming how existing genes are read, not by inventing new genes from scratch.

References: NHGRI, Epigenomics Fact Sheet · NHGRI Genetics Glossary: Epigenetics

Gregor Mendel’s Laws of Genetics

Children inherit genetic material from their parents. Inheritance follows structured biological rules, not unlimited variation.

Reference: Gregor Mendel and the Principles of Inheritance

The E. Coli Experiment (Richard Lenski)

In Richard Lenski’s long-term E. coli evolution experiment, one population eventually gained the ability to metabolize citrate in the presence of oxygen, a trait normally absent in E. coli. Lenski’s team published in Nature (2012) showing the trait arose through a gene duplication that placed the existing citT transporter under a new promoter active in oxygenated conditions.

Lenski interpreted this as evolutionary innovation. A cautious reading is that a pre-existing transporter was rewired through regulation. That supports adaptation, but it is a weaker example for the origin of entirely new molecular machinery.

Reference: Blount et al., Nature (2012), Genomic analysis of a key innovation in Lenski’s experiment

The Cambrian Explosion

Around 541 million years ago, many major animal body plans appear in the fossil record over a geologically short interval (roughly 13-25 million years).

This pattern is often presented as a challenge to strictly slow, uniform evolutionary change.

Want to go deeper?

Full-length lectures: Oxford University Museum, Prof. Paul Smith · PBS Eons, “Could You Survive The Cambrian Explosion?”

A Parallel Critique, The Origin of Life

The Cambrian Explosion challenges the idea that complex body plans arose by slow, unguided change. A related challenge comes earlier in the story: the origin of life itself. Prof. James Tour (Rice University), a leading synthetic organic chemist, argues that current chemistry has not explained how life could start from non-living matter.

Neanderthals, A Human People

Neanderthals (Homo neanderthalensis) were a human population that lived across Europe and western Asia from roughly 430,000 to about 40,000 years ago. Modern genetics, archaeology, and anatomy now show them as fully human, not as an “ape-like ancestor.”

Reconstruction of a Neanderthal face.

Neanderthal (left) compared with a modern human (right).

Why specialists describe them as human:

• Same human genus Homo, often treated as a subspecies (Homo sapiens neanderthalensis).
• Brains as big as ours or larger (~1,500–1,600 cc vs. modern ~1,350 cc).
• Complex tools, fire, cooking, and intentional burials with grave goods.
• Symbolic art, cave paintings in Spain dated to ~64,000 years ago, pre-dating Homo sapiens in Europe (Hoffmann et al., Science, 2018).
• Same FOXP2 “language gene” variant as modern humans (Krause et al., Current Biology, 2007).
• Interbred with Homo sapiens, all non-African people carry 1–4% Neanderthal DNA (Green et al., Science, 2010; Prüfer et al., Nature, 2014). Populations that interbreed and produce fertile descendants belong to the same human family.

References

1. Green, R. E., et al. (2010). A draft sequence of the Neanderthal genome. Science 328(5979): 710–722. DOI · PubMed
2. Prüfer, K., et al. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43–49. DOI
3. Hoffmann, D. L., et al. (2018). U-Th dating of carbonate crusts reveals Neandertal origin of Iberian cave art. Science 359(6378): 912–915. DOI · PubMed
4. Hardy, K., et al. (2012). Neanderthal medics? Evidence for food, cooking, and medicinal plants entrapped in dental calculus. Naturwissenschaften 99: 617–626. DOI
5. Krause, J., et al. (2007). The derived FOXP2 variant of modern humans was shared with Neandertals. Current Biology 17(21): 1908–1912. DOI
6. Smithsonian National Museum of Natural History, Homo neanderthalensis.
7. Natural History Museum (London), Who were the Neanderthals?

The Transition Question

Regardless of how far back we examine the fossil record, humans appear consistently as human (with human DNA), and apes appear as apes (with ape DNA).

Here’s a much simpler, shorter version:

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The key question is: do fossils show slow, step-by-step change, or long periods where little changes followed by sudden (appearance) of new forms? This idea was suggested by Stephen Jay Gould.

A clear example is the Cambrian Explosion, a period when many distinct life forms appeared in a relatively short time, casting serious doubt on the claim that evolution always proceeds slowly and continuously.

The Cambrian case is a clear example. Taken together with other discontinuities in the fossil record, it makes a strictly slow-and-continuous model highly implausible.

Likewise, many argue that the limited number of clear transitional forms in key lineages remains a serious unresolved issue for fully gradual accounts.

The Origin of Sexual Reproduction

Human reproduction needs both sperm and egg. A child gets about 50% of nuclear DNA from the father and 50% from the mother. This raises a hard question: how did male and female systems develop together and still work at each step?

That is why many biologists see the origin of sex as one of evolution’s hardest questions. Sex has a big cost compared with asexual reproduction, but it is still common in complex life. So any unguided explanation has to show two things: why sex was selected despite the cost, and how linked systems like meiosis, matching gametes, and sex determination appeared step by step.

Reference: Goodenough U. & Heitman J. (2014). Origins of Eukaryotic Sexual Reproduction. Cold Spring Harbor Perspectives in Biology.