Why chance and necessity can't be trusted with the puzzles of the origin of life.

People Can Do Puzzles — And Why That matters

Eric Hedin 

Occasionally, during the winter months, my family enjoys doing a jigsaw puzzle. We recently completed two 1,000-piece puzzles. If you’ve ever worked on one of these puzzles, when you first dump the pieces in a jumble onto the table, it can seem like a daunting task. With persistence, however, the thing begins to come together. 

Our ability to complete a puzzle hinges upon clues that are unavailable to nature, were natural processes given the task of assembling the puzzle. Assembling proteins, DNA, and other molecular components of a living cell are the puzzles of nature. Why do I say this?

Clue #1: We are given a clear picture of how the completed puzzle should look. The picture on the puzzle box gives the overarching meaning or purpose for the many interlocking pieces. Nature has no teleological picture of how things should turn out. Whatever nature attempts to assemble is done blindfolded, without foresight. What difference would this make? Just imagine trying to put together a jigsaw puzzle without having a clue about how the completed picture should look. I suppose some intrepid puzzle enthusiasts might attempt this, but without the end goal in view, progress would at best be painstaking, tentative, and slow.

Clue #2: We can constantly visually examine each piece to observe its relationship to other pieces. These visual clues include information about the shape and orientation of the puzzle piece cutouts that allow it to uniquely connect with its neighboring pieces. We also have available to us the visual clues of the image fragments on each piece, helping us to quickly discern if a given piece matches others.

Very Picky About Relationships

What does nature have available to it, when attempting to assemble a system such as a complex biomolecule? The nature of chemical bonding will allow some “pieces” to be selected, while excluding others. But nature has no clues concerning which atom or molecule, among those that could bond, is the appropriate one to bring the project closer to a particular end result. End results, such as functional proteins, are known to be very picky when it comes to getting the right relationships among the component pieces.

To better understand the handicap nature plays with, imagine trying to complete a puzzle blindfolded! Undaunted, someone might maintain that it could still be done, however tediously, by trying one piece after another, until your sense of touch informed you that you had found the piece that uniquely fit with its neighbor. Some puzzles are designed this way, where only one piece has the appropriate cutouts to fit in a particular location. However, what if multiple different pieces had the same shape, but only one piece had the correct image to match the pattern building up to form the predetermined completed picture? Your sense of touch would be insufficient. The tactile clues for which piece to insert next couldn’t supply you with the necessary information. Getting the right pieces assembled in the right arrangement to produce the right final picture would be reduced to luck. 

What’s the Chance of That?

Let’s start with a simple puzzle with a child’s level of difficulty, having only 60 pieces. Trying to assemble it blindfolded, not knowing what the final image is, and wearing mittens so that you can’t feel the cutout shapes makes this “simple” task impossible. Let’s see why. 

The first piece is “free.” Then you have 59 choices for the second piece. If, by luck you got it right, you would then have 58 choices for the third piece, and so on. So, the probability of getting all the pieces assembled correctly is 1:59! That is, 59 factorial, which works out to about 1 chance in 1080. This is equivalent to finding one unique proton out of all the protons in the entire universe! These impossibly small odds are for something that is merely “child’s play” for a normally intelligent human.

Humans Can Do Puzzles

The point here is not really to ponder how improbable it would be for natural processes to correctly assemble a jigsaw puzzle (and admittedly, the real odds would be much smaller than calculated in the paragraph above, since each piece has two sides and each piece has a continuous degree of orientations it could be rotated through in order to properly fit it into place). The point is that humans can do puzzles. This has consequences for our picture of reality. Under a materialistic view, holding that nothing exists except the matter and energy and spacetime of our universe, the inescapable, but absurd, conclusion is that natural processes can correctly assemble jigsaw puzzles.

Under the materialistic view, natural processes gave rise to humans (as a sort of intermediate step to the completed puzzle), and humans then put together puzzles (as well as cars and computers and cities). So, from beginning to end, the materialist must believe that the primordial hydrogen plasma of the universe, governed by nothing other than the laws of physics, will in just a few billion years turn into humans who do jigsaw puzzles!

The power of intelligence is remarkable. What could never happen by the unguided operation of the forces of nature acting on matter, is done as a relaxing pastime by intelligent humans. If this unnatural accomplishment seems a puzzle to the materialist, then perhaps a different perspective is in order. Since our intelligence instantiates outcomes (cars, computers, cities, and puzzles) that cannot arise by unguided nature, then our humanness cannot be naturally derived either. A view of reality that embraces an intelligent mind behind the universe corresponds most reasonably to the big picture that emerges when we properly fit together all the puzzling pieces of our existence.

File under "well said." XCVI

 "Whenever you find yourself on the side of the majority, it is time to reform (or pause and reflect)."

Mark Twain.

On using stats for illumination rather than support?

 Ross Pomeroy Reminds us of P-Value Problems

Cornelius G Hunter 

Ross Pomeroy’s Article in yesterday’s Real Clear Science was a much needed reminder about the dangers of statistical hypothesis testing. But while Pomeroy rightly points out important problems, particularly with the so-called P-value, out here on the ground, the problem is much worse.

One of Pomeroy’s several legitimate concerns is the use of what is essentially a default value of 0.05 for P. Too often scientists don’t realize that, as David Colquhoun has pointed out, this will lead to false conclusions at least 30 percent of the time. Pomeroy also points out the common fallacy of interpreting the P value as the probability that the null hypothesis is true.

The result of such mishandling of hypothesis testing is that, “Quite simply, a large amount of published research is false.” 

                     The result of such mishandling of hypothesis testing is that, “Quite simply, a large amount of published research is false.”

Would that it would end there. Unfortunately, when it comes to evolutionary studies, fixing these problems is like rearranging the deck chairs on the Titanic. These concerns about selecting a good alpha value and understanding the nuances of what P actually means, while important, pale in comparison to a much larger infraction: using the P-value to mask what is, in fact, a strawman argument.

One of the key, underlying, assumptions in using the P-value is that there are only two alternatives, the null and alternative hypotheses. These two hypotheses must be complementary—they must be distinct, mutually exclusive, and exhaustive. In other words, one of them must be true, and the other must be false. They cannot both be true, or both be false. They cannot overlap, and there can be no other possibilities.

And while such a perfect pair of hypotheses is possible in simple academic problems such as colored marbles in an urn, real world problems often are more complicated. Take something as seemingly simple as the question of whether or not it will rain today. Is it not binary? Either it will rain, or it will not rain. Right?

Well no. The weather has a multitude of complexities. It is spatially and temporally varying, with an infinite degree of variation. What if it sprinkles? What if the rain evaporates before it reaches the ground? How do you define the time and location? What if it rains in one location but not another?

What the P-value, and its null hypothesis, allows is for trivial null hypotheses to be erected and easily knocked down like strawmen, thus “proving” ones favored explanation. 

Curtains for the selfish gene?

 New Book Puts Richard Dawkins’s “Selfish Genes” in the ICU

Emily Reeves 

Biologist Richard Dawkins came to prominence in 1976 with his Book The Selfish Gene. Nearly half a century later, we’re entitled to wonder how the work has held up. In his recent book, Selfish Genes in ICU?, Dr. Michael Jarvis considers that question, asking whether recent findings in biology match the predictions of Dawkins’s selfish gene concept.

Jarvis, who holds a PhD in biology from the University of Cape Town (where he focused on zoology), takes his reader on a historical journey. He first describes the origin of the universe and the history of Earth, and moves on to Darwin’s theory of evolution. Here, he outlines four key points in The Origin of Species, while paying special attention to one challenge Darwin faced: the Cambrian explosion. From there, Jarvis describes Dawkins’s selfish gene concept — the idea that a gene can be seen as a “selfish unit” that exploits an organism to carry out its own process of replication. Stated another way, the selfish gene concept holds that natural selection takes place at the gene level.

In subsequent chapters Jarvis dives into some discoveries that (spoiler alert!) don’t really match with the selfish gene idea. Jarvis does a nice job of laying out the evidence so that the reader can decide what to think.

                          

Teaser on the Human Eye

One of my favorite parts of the book is the sections on biological function and complexity. I won’t give it all away, but here’s a teaser from the section on the human eye:

                      In the past some scientists suggested that the human eye retina was actually a poor design. Richard Dawkins proposed this argument. In his 1986 book The Blind Watchmaker he concluded that the vertebrate eye is functionally sub-optimal because the retina photoreceptors are oriented away from incoming light.

                        Jarvis addresses head-on this frequently repeated claim of poor design. He goes on to cite recent discoveries and explains how this new research affects our understanding of the purported “sub-optimal” design. He notes that our retinas contain special Müller cells which funnel light through the optic nerve onto the retina, compensating for any loss of vision related to the “backwards wiring” of the vertebrate retina:

                      Research by Amichai Labin and Erez Riba from Israel’s internationally recognized Technion – Israel Institute of Technology in Haifa has shown that the surface of the retina also has so-called Müller cells. These cells not only compensate for the light sensitive receptors being “back to front.” Their function actually results in vision being better than it would have been if the light sensitive cells had been the so-called “right-way round.”

                               To learn more about the complexity of the eye you can read my article here or Casey Luskin’s article here.

                        

An Update on Two Decades

In the final chapters of the book, Dr. Jarvis updates his reader on what the last twenty years have revealed about evolution. His focus here is on the study of epigenetics, orphan genes, Hox genes, mitochondrial DNA, and directed mutagenesis, all shedding light on how genes evolve and whether or not they are units of selection. Throughout, he argues that these recently discovered genetic features don’t fit the selfish gene concept. 

Here’s one example from the field of epigenetics. Epigenetics is the study of mechanisms that change gene expression but that are not heritable. Epigenetic mechanisms allow for both behavior and the environment to affect how a gene works. Here’s the problem epigenetics poses for selfish genes: if a gene is the unit of selection, what benefit does a non-heritable change that is only evidenced in the organism have for the unit of selection? Why would such a mechanism ever be selected in the first place? Hence, epigenetics only makes sense in a system-wide context.

Let’s look at one more of Jarvis’s examples: master regulatory genes, aka Hox genes. These genes have the purpose of being master regulators within a system context. Their activation and function depend upon upstream and downstream genes respectively. A master regulatory gene is helpless without its system context. How then could such a gene be a unit of selection? Do master regulatory genes really desire to reproduce more than they do to serve the organism? Is there evidence for that? Definitely not.

Into the Melting Pot

In gentle fashion, Jarvis lays out numerous pieces of evidence that jeopardize Dawkins’s view that genes are selfish and act as the units of selection. That makes this book the perfect gift for an inquisitive friend who might not be familiar with some of the recent challenges to Dawkins’s ideas. 

Jarvis concludes that “selfish genes are in the ICU” and he encourages the reader to place recent discoveries into what he calls a melting pot — a place where many different people and ideas exist and often produce something new. He concludes with a question to the reader: “Are you and I ready for a new theory of evolution that may be as difficult to accept as were the revelations of Albert Einstein?”