Biologic
Perspectives

The Mismeasure of Man: Why Popular Ideas about Human-Chimp Comparisons Are Misleading or Wrong

By Ann Gauger

 You have probably heard that our DNA, the stuff that makes us human, is only 1% different from chimps. The claim that we are little more than apes is now part of the Zeitgeist of our culture, having been propagated in the popular press for nearly 40 years. However, that statement and the conclusions drawn from it are false.

Let’s look at the first claim, that we are only 1% different from chimps. That measurement only compares base changes in human and chimp DNA. It doesn’t include other kinds of changes to the DNA, like deletions and insertions or rearrangements. In addition, because of the sequencing methods used, repetitive DNA is not included.

Now that complete or nearly complete genome sequences for humans and chimps are available, a better picture of our differences and similarities is emerging. A 2007 essay in the journal Science, “Relative Differences: The Myth of 1%,” says this (the pdf is here ):

Researchers are finding that on top of the 1% distinction, chunks of missing DNA, extra genes, altered connections in gene networks, and the very structure of chromosomes confound any quantification of “humanness” versus “chimpness.”

To be specific, in addition to the 1% distinction already noted, entire genes are either duplicated or deleted between the two species, sometimes in long stretches called segmental duplications. Such duplications represent a 6.4% difference between chimps and humans. There are also insertions and deletions within genes, which affect the structure and function of the proteins they encode. That contributes another 3%, according to some estimates. And there are entirely new genes, specific to humans.

There are also changes that affect the timing and amount of gene expression. These changes include the insertion of new regulatory sequences upstream of genes. For example, some 6% of our genome is unique Alu insertions, as they are called. And Alu sequences are known to affect gene expression.

In addition, there are human-specific increases in DNA methylation that affect gene expression in the brain, and increased RNA modifications in the brain. These changes would not be detected by simply comparing DNA sequences. Yet they affect gene expression and interaction. Indeed, by one measure, 17.4% of gene regulatory networks in the brain are unique to humans.

Then there are DNA rearrangements. How genes are organized along chromosomes, and even the chromosomes structures themselves can be different. Our Y-chromosomes are strikingly different from those of chimps, for example. This was a surprise to researchers, given the relatively short time our species supposedly diverged from one another. Rearrangements are also not included in the 1% number, and are difficult to quantify.

It should be apparent that we are only beginning to discover important differences between chimps and us, so our numbers are incomplete. In fact, there is no clear way even to count the changes. Beyond that, we do not even know yet how many or which of these differences are functionally important. Perhaps not all are. However, it would be a mistake (one that has been made before) to assert that none of them are functionally significant, as the Encode project demonstrated.

From the same Science paper: 

Could researchers combine all of what’s known and come up with a precise percentage difference between humans and chimpanzees? “I don’t think there’s any way to calculate a number,” says geneticist Svante Pääbo, a chimp consortium member based at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “In the end, it’s a political and social and cultural thing about how we see our differences.” [Emphasis added.]

Indeed. In the end, despite our inability to quantify them, the differences matter. You can have two houses built of the same materials — two by fours, pipes, wall board, nails, wires, plumbing, tile, bricks, and shingles — but end up with very different floor plans and appearances, depending on how they are assembled. So it is with us. We may have almost the same genes as chimps, but the timing and distribution of their expression are different, and matter in significant ways.

It should be said that many scientists are aware of these distinctions. What I have said here about differences between chimps and humans is derived from the scientific literature. In fact, the NIH recently recommended that chimps not be used as a model for medical research, precisely because we are different in many ways. Yet somehow these differences do not seem to make it into popular literature or TV shows. 

Here are some large-scale differences that get overlooked in the drive to assert our similarity. Our physiology differs from that of chimps. We do not get the same diseases, our brain development is different, even our reproductive processes are different. Our musculoskeletal systems are different, permitting us to run, to throw, to hold our heads erect. We have many more muscles in our hands and tongues that permit refined tool making and speech.

Going beyond the physical, we have language and culture. We are capable of sonnets and symphonies. We engage in scientific study and paint portraits. No chimp or dolphin or elephant does these things. Humans are a quantum leap beyond even the highest of animals. Some evolutionary biologists acknowledge this, though they differ in their explanations for how it happened.

 And that brings me to another false assumption underlying the mismeasure of man — that genes make us who we are. Many things beyond our genes contribute to making us who we are. Our genes do not control us. Certainly, they can influence our predisposition to disease, the shape of our nose, or the color of our eyes, but they do not specify how we will respond to the challenge of disease, or what spouse we will choose. Our experience and our moral character have something to contribute to those things. New studies in psychology indicate, for example, that we can rewire our own brains to think in new patterns; those new thoughts actually change the underlying neural connections. The choices we make matter. And this is a very non-Darwinian thought.

The documentary The War Against Humans and Wesley Smith’s companion e-book show how some people seek to equate us with animals, based in part on the false assumptions described above. They see humanity as a destructive species, even a scourge upon the earth that needs to be destroyed. In truth, though, we are a unique, valuable, and surprising species with the power to influence our own futures by the choices we make. If we imagine ourselves to be nothing more than animals, then we will descend to the level of animalism. It is by exercising our intellects, and our capacity for generosity, foresight, and innovation, all faculties that animals lack, that we can face the challenges of modern life.

BIO-Complexity in Review

By Ann Gauger

Here are links to the published articles all in one place, in case you missed something.

You will notice certain themes recur:

  • Evolutionary algorithms succeed only because of active information.
  • The origin of new protein folds and new protein functions continues to cause a problem for evolution.
  • The organizational and information-bearing properties of the genetic code are not explained by Darwinian processes.
  • Old ideas in biology— anthropocentrism, structuralism and second law problems—gain a fresh hearing.

And new ideas are advanced:

  • Design in biology is as much about what isn’t done as what is done.
  • The sequence-structure-function relationship found in biology— where a linear DNA code translates to a 3D protein, which in turn produces a biological function— has an analogy in human language, namely  Chinese ideograms. With the proper tweaking this analogy can be exploited to test what random changes to code (that writes Han characters) does to the functional product. Enter Stylus, a computational model for testing evolution.

The links are live, so go explore.

2013 

Active Information in Metabiology   Winston Ewert, William A. Dembski, Robert J. Marks II

The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism             Michael J. Denton

The Place of Life and Man in Nature: Defending the Anthropocentric Thesis                       Michael J. Denton

Entropy and Evolution   Granville Sewell

2012

A Tetrahedral Representation of the Genetic Code Emphasizing Aspects of Symmetry   Fernando Castro-Chavez

Climbing the Steiner Tree—Sources of Active Information in a Genetic Algorithm for Solving the Euclidean Steiner Tree Problem   Winston Ewert, William A. Dembski, Robert J. Marks II

Lignin—Designed Randomness   Matti Leisola, Ossi Pastinen, Douglas D. Axe

Time and Information in Evolution   Winston Ewert, William A. Dembski, Ann K. Gauger, Robert J. Marks II

2011

A Stylus-Generated Artificial Genome with Analogy to Minimal Bacterial Genomes    Douglas D. Axe, Philip Lu, Stephanie Flatau

The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway   Ann K. Gauger, Douglas D. Axe

Can the Origin of the Genetic Code Be Explained by Direct RNA Templating?   Stephen C. Meyer, Paul A. Nelson

2010 

The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations    Douglas D. Axe

A Vivisection of the ev Computer Organism: Identifying Sources of Active Information   George Montañez, Winston Ewert, William A. Dembski, Robert J. Marks II

Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness   Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, Ralph Seelke

The Case Against a Darwinian Origin of Protein Folds   Douglas D. Axe

Intelligent Design Research: BIO-Complexity 2013

By Ann Gauger

The most recent article published in BIO-Complexity considers the wild and abstruse world of metabiology, a theoretical computational attempt to model evolutionary biology. Dr. Gregory Chaitin began the work in 2009, and it has progressed to the point described in his 2012 book Proving Darwin, shown below. The question is, does his model succeed?

image

Winston Ewert, William Dembski and Robert Marks II take on that question in their article in BIO-Complexity, whose abstract is below. I will let them speak for themselves.

Active Information in Metabiology
Winston Ewert, William A. Dembski, Robert J. Marks II

Abstract

Metabiology is a fascinating intellectual romp in the surreal world of the mathematics of algorithmic information theory. In this world, halting oracles hunt for busy beaver numbers and busy beaver numbers unearth Chaitin’s number, knowledge of which in turn allows resolution of numerous unsolved mathematical problems, many of whose solutions would earn large cash bounties. All this, despite the fact that halting oracles can’t be implemented on a computer, a computer can never make a list of busy beaver numbers, and Chaitin’s number, always a positive real number less than one, is proven to be unknowable. The fun of metabiology is the application of these ideas to illustrate Darwinian evolution. When metabiology’s evolutionary process is stripped of the glitter of algorithmic information theory, however, what remains is a procedure similar to that used in other attempts to model Darwinian evolution, like the ev and AVIDA computer programs. Metabiology, like ev and AVIDA, succeeds because available sources of knowledge about the solution being sought can be mined. We show the mining of information from a halting oracle has striking similarities to mining information from a simple Hamming oracle. Unlike a halting oracle, however, Hamming oracles can be implemented on a computer. We demonstrate that for both oracles, information can be mined by search strategies that are analogous in some respects even though the methods differ; in both cases the search strategy used greatly influences the result. Because metabiology’s process relies on unknowable numbers and infinite resources, its reported relative performance measures can only be expressed asymptotically. That is, the results of metabiology are only proven to be true on the largest possible scale. In fact, simple simulations using bounded resources suggest the asymptote is not always approached quickly, indicating that metabiology results may only hold for scales larger than any practical system.

Intelligent Design Research: BIO-Complexity 2013

By Ann Gauger

Entropy and Evolution

image

The second law of thermodynamics sounds imposing, but the idea is simple. It was originally framed in terms of  thermal entropy, and can be stated  thus: In a closed system, entropy tends to increase.

That means, in a closed system where there are local hot and cold spots, eventually the whole system will reach a state where everything is the same temperature.

The second Law also has been used to explain the tendency of all things to go from order to disorder. Left unattended, things break down. And conversely, things don’t spontaneously organize themselves into complex structures unless they are receiving input from somewhere. Think about 747 jets for example. You can wait a thousand million years and a jet will not assemble itself from parts, even if a tornado blows through. But try it the other way—put a jet on a tarmac in Kansas and wait a thousand years, and you will see entropy at work, even without the tornado.

The second Law has been used as an argument against unguided evolution:  life cannot spontaneously self-assemble without input from the outside, because such a striking increase in order violates the second Law. The rebuttal usually comes by saying that the planet Earth is not a closed system, because it receives energy from the sun.

How to unweave this brangle? In the recent paper from BIO-Complexity, the mathematician Granville Sewell takes on the topic in a way that should be accessible to most. If you want to find out how he handles tornados, you will have to read the paper!

Read More

Intelligent Design Research: BIO-Complexity 2013

By Ann Gauger

Michael Denton is the author of our third article in the continuing series on research and critical review articles published in BIO-Complexity in 2013. Here Denton addresses the question, “Are there laws of form (or Types) in biology? And what is their source?” The idea that there are underlying rules that govern biological structures, rules that cannot be explained by natural selection, is very old, and pre-dates Darwinism. He presents the classical reasons for the idea of Structuralism, and  explains how Pan-selectionism, the belief that natural selection can explain everything in biology, came to dominate biologists’s thinking. He then describes how recent research is tipping things back the other way. 

image

Abstract pattern is ubiquitous throughout the living realm. This image of radiolarian shells is taken from Plate 31 of Ernst Haeckel’s Kunstformen der Natur (Artforms of Nature),1904.

The Types: A Persistent Structuralist Challenge
to Darwinian Pan-Selectionism

Michael J. Denton1,2 *
1Aditya Jyot Eye Hospital, Mumbai, INDIA
2Discovery Institute, Seattle, Washington, USA

Abstract
Here I first review the structuralist or typological world view of pre-1859 biology, and the concept that the basic forms of the natural world—the Types—are immanent in nature, and determined by a set of special natural biological laws, the so-called ‘laws of form’. I show that this conception was not based, as Darwinists often claim, on a priori philosophical belief in Platonic concepts, but rather upon the empirical finding that a vast amount of biological complexity, including the deep homologies which define the taxa of the natural system, appears to be of an abstract, non-adaptive nature that is sometimes of a strikingly numerical and geometric character. In addition, these Types exhibit an extraordinary robustness and stability, having in many instances remained invariant in diverse lineages for hundreds of millions of years. Second, I show that neither Darwinism nor any subsequent functionalist theory has ever provided a convincing adaptive or functionalist explanation for the Types or deep homologies. Third, I discuss how recent advances have provided new support for the structuralist notion that the basic forms of life are immanent in nature. These include the discovery of the cosmic fine tuning of the laws of nature for life as it exists on earth, and advances in areas of molecular and cellular biology, where it is apparent that a considerable amount of biological complexity is clearly determined by the self-organizing properties of particular categories of matter, rather than being specified in detail in a genetic blueprint as functionalism demands.


Denton MJ (2013) The Types: A persistent structuralist challenge to Darwinian pan-selectionism. BIO-Complexity 2013 (3):1−18. doi:10.5048/BIO-C.2013.3

Is Nature Designed For Us?

By Ann Gauger

imageSmithsonian/Flicker http://flic.kr/p/5tRFwT

From the paper by Michael Denton, called “The place of life and man in nature: Defending the anthropocentric hypothesis”:

"The question of questions for mankind—the problem which underlies all others, and is more deeply interesting than any other—is the ascertainment of the place which mankind occupies in nature and of his relations to the universe of things."             – Thomas Huxley, Man’s Place in Nature 

For centuries the traditional teleological anthropocentric framework provided the answer to Thomas Huxley’s “question of questions.” But following the Copernican revolution and particularly after the publication of Darwin’s On the Origin of Species, the traditional framework was seen to be increasingly untenable; mankind, so it seemed, had no special place in nature. However, as I show, discoveries in chemistry and biochemistry in the 19th  and early 20th  centuries, and in cosmology and fundamental physics and comparative physiology during the course of the 20th  century, have reopened the ‘grand debate’ by providing intriguing new support for the old and seemingly obsolete anthropocentric paradigm.

Intelligent Design Research: BIO-Complexity 2013

By Ann Gauger

In our second article in the series we present a paper by Michael Denton, who is well known for his seminal work Evolution: A Theory in Crisis. Here he lays out arguments from physiology and biochemistry to show that the behaviors of basic chemical molecules like oxygen, water, and carbon dioxide  are uniquely suited for living beings like ourselves.

The Place of Life and Man in Nature: Defending the Anthropocentric Thesis

Michael J. Denton

Abstract

Here I review the claim that the order of nature is uniquely suitable for life as it exists on earth (Terran life), and specifically for living beings similar to modern humans. I reassess Henderson’s claim from The Fitness of the Environment that the ensemble of core biochemicals that make up Terran life possess a unique synergistic fitness for the assembly of the complex chemical systems characteristic of life. I show that Henderson’s analysis is still remarkably consistent with the facts one century after it was written. It is still widely accepted even among researchers in astrobiology. I also review the evidence for believing that many of the properties of the same core set of biochemicals are specifically fit for the physiology of complex terrestrial beings resembling modern humans. I show that none of the recent advances in the field of extremophile biology, alternative biochemistries, or recent allusions to apparent defects in the fitness of nature for Terran life significantly undermine the core argument, that nature is peculiarly fit for carbon-based Terran life, and especially for the physiology of complex terrestrial beings resembling modern humans.

Denton MJ (2013) The place of life and man in nature: Defending the anthropocentric thesis. BIO-Complexity 2013 (1):1–15.

doi:10.5048/BIO-C.2013.1

Intelligent Design Research: BIO-Complexity 2013

By Ann Gauger

We are beginning a series highlighting work published this year in the on-line journal BIO-Complexity. All articles are freely accessible, and address questions relevant to intelligent design theory from a variety of points of view. This first critiques a theoretical construct called metabiology that seeks to demonstrate evolution by using algorithmic information theory.

Active Information in Metabiology

Winston Ewert,1* William A. Dembski,2 Robert J. Marks II1
1Electrical & Computer Engineering, Baylor University, Waco, Texas, USA
2Discovery Institute, Seattle, Washington, USA

Abstract
Metabiology is a fascinating intellectual romp in the surreal world of the mathematics of algorithmic information theory. In this world, halting oracles hunt for busy beaver numbers and busy beaver numbers unearth Chaitin’s number, knowledge of which in turn allows resolution of numerous unsolved mathematical problems, many of whose solutions would earn large cash bounties. All this, despite the fact that halting oracles can’t be implemented on a computer, a computer can never make a list of busy beaver numbers, and Chaitin’s number, always a positive real number less than one, is proven to be unknowable. The fun of metabiology is the application of these ideas to illustrate Darwinian evolution. When metabiology’s evolutionary process is stripped of the glitter of algorithmic information theory, however, what remains is a procedure similar to that used in other attempts to model Darwinian evolution, like the ev and AVIDA computer programs. Metabiology, like ev and AVIDA, succeeds because available sources of knowledge about the solution being sought can be mined. We show the mining of information
from a halting oracle has striking similarities to mining information from a simple Hamming oracle. Unlike a halting oracle, however, Hamming oracles can be implemented on a computer. We demonstrate that for both oracles, information can be mined by search strategies that are analogous in some respects even though the methods differ; in both cases the search strategy used greatly influences the result. Because metabiology’s process relies on unknowable numbers and infinite resources, its reported relative performance measures can only be expressed asymptotically. That is, the results of metabiology are only proven to be true on the largest possible scale. In fact, simple simulations using bounded resources suggest the asymptote is not always approached quickly, indicating that metabiology results may only hold for scales larger than any practical system.

Ewert W, Dembski WA, Marks II RJ (2013) Time and information in evolution. BIO-Complexity 2013 (4):1–19. doi:10.5048/BIO-C.2013.4