The Biologic hood ornament is back!
Styled after kinesin, Motor Trend Motor Molecule of the Year, our signature hood ornament started as a joke (believe it or not). A few of us mounted these winged beauties on our cars back in 2009 as a way of raising public awareness of molecular machines and their aesthetic value. Well, we were completely unprepared for the response. Once a few of these bad boys got out on the road we were inundated with requests, to the point that our supplier couldn’t keep up.
With the supply issues now resolved, we are pleased to say that we expect to be able to take new orders shortly. Thanks for your patience… and happy first of April!
Credits
By Ann Gauger
The co-discoverer of the theory of evolution by natural selection, Alfred Russel Wallace, didn’t think human evolution could be explained solely in terms of Darwinian processes, at least as far as human cognition and behavior was concerned. And it cost him his scientific reputation.
Varki, Geschwind and Eichler [1] summarize it this way:
Wallace lost favour with the scientific community partly because he questioned whether natural selection alone could account for the evolution of human mind, writing: “I do not consider that all nature can be explained on the principles of which I am so ardent an advocate; and that I am now myself going to state objections, and to place limits, to the power of ‘natural selection’. How could ‘natural selection’, or survival of the fittest in the struggle for existence, at all favour the development of mental powers so entirely removed from the material necessities of savage men, and which even now, with our comparatively high civilization, are, in their farthest developments, in advance of the age, and appear to have relation rather to the future of the race than to its actual status?”
Although Wallace was criticized for apparently invoking spiritual explanations, one of his key points remains valid — that it is difficult to explain how conventional natural selection could have selected ahead of time for the remarkable capabilities of the human mind, which we are still continuing to explore today. An example is writing, which was invented long after the human mind evolved and continues to be modified and utilized in myriad ways. Explanations based on exaptation seem inadequate, as most of what the human mind routinely does today did not even exist at the time it was originally evolving. Experts in human evolution or cognition have yet to provide a truly satisfactory explanation. Thus, ‘Wallace’s Conundrum’ remains unresolved: “[…] that the same law which appears to have sufficed for the development of animals, has been alone the cause of man’s superior mental nature, […] will, I have no doubt, be overruled and explained away. But I venture to think they will nevertheless maintain their ground, and that they can only be met by the discovery of new facts or new laws, of a nature very different from any yet known to us.” [2]
1. doi:10.1038/nrg2428
2. Internal citations have been removed for clarity, and emphasis added. The quotations from Wallace are taken from Wallace, AR (1870) Contributions to the Theory of Natural Selection. A Series of Essays (Macmillan, London).
By Ann Gauger
You’ve probably all heard the statement somewhere that we are 98-99% identical in our DNA sequence to chimps. Although the number has been revised downward as more detailed comparisons are made, a recent estimate still says we are 96% identical [1]. We also have significant similarity to gorillas and to orangutans [2].
When we look at the level of physiology, anatomy, reproduction, cognitive capacity, and behavior, though, we are much more different from great apes than these DNA comparisons might suggest. There are numerous traits that distinguish us from great apes, though that is not what the popular science articles emphasize. Care to guess how many?
Would you believe hundreds? In 2005 a partial list of traits that distinguish us from great apes was published [1]. I won’t list them here, but I would like to point out that the differences are not minor. Many of them raise questions about the suitability of great apes as models for human disease. Our organ physiology, biochemistry, and endocrinology are different. Our susceptibility to diseases such as AIDs, malaria, hepatitis B/C and influenza A are different. Our neurobiology is different, not only in brain size, but in density of neurons and synapses. Our reproduction and development are different. For example, human infants require extended care after birth. This is in part because infant brains are still growing rapidly and forming new synapses, then remodeling connections as they learn. Even adult humans can grow new neurons. Most significantly, though, our behavior, cognitive capacity, communication, social organization and culture are radically different from great apes—81 differences listed for these categories alone.
Can Darwinian natural selection account for all this? I have my doubts, for reasons to be discussed.
1. Varki A, Altheide TK (2005) Comparing the human and chimpanzee genomes: Searching for needles in a haystack. Genome Res. 15:1746-1758.
2. Hobolth A, Dutheil JY, Hawks J et al. (2011) Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res. 21: 349-356.
By Doug Axe
According to Darwin, all living things are related in the strict sense of a having a shared family tree. But there’s a more general and obvious sense in which living things are related. It’s the sense of having noteworthy similarities—the sense in which snowboarding, skateboarding, and wakeboarding are related (or iPhones and iPads, or Jupiter and Saturn). So, how do we know whether living things are really all related in the strict sense?
Until recently, the answer was that a real family tree should generate a fully consistent pattern of similarities. For example, we are told that chimps and humans came from the same ancestral stock (call it CH stock) and that gorillas, chimps and humans all came from an earlier ancestral stock (GCH stock). If so, then the human and chimp genomes should consistently be more similar to each other than either is to the gorilla genome, since the human and chimp histories were one and the same thing more recently than the human and gorilla (or chimp and gorilla) histories were.
Well, the recent publication of the gorilla genome sequence shows that the expected pattern just isn’t there. Instead of a nested hierarchy of similarities, we see something more like a mosaic. According to a recent report [1], “In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other…”
That’s sufficiently difficult to square with Darwin’s tree that it ought to bring the whole theory into question. And in an ideal world where Darwinism is examined the way scientific theories ought to be examined, I think it would. But in the real world things aren’t always so simple.
1. doi:10.1038/nature10842
Okay, it’s more art than science. The blobby glass thing shows the outer shape of the enzyme (luciferase) that causes fireflies to glow, with the bright object in the cavity representing the filament-like molecule (luciferin) that actually produces the light. It’s cool on every level—from the biochemistry on up to the sight of a moonlit field pulsing with fireflies. Reasoning in reverse from Darwinism, we infer that it must be easy to get these molecular lanterns by accident because many different versions exist in a wide variety of life forms. But they aren’t nearly as simple as the image suggests. The outer shape may look like a blob, but a highly refined inner structure is needed for that enzyme to hold together and do its job, and the same is true for the other enzymes that make the various luciferins. Reverse reasoning tries to tease out historical details by assuming that the processes in operation have been correctly identified and understood. There’s certainly a place for that in science, but it always has to be checked against forward reasoning, where we test whether we really have identified the right processes. Darwinism seems to have failed this test, but biologists won’t see this until they shift out of reverse.
Doug
By Doug Axe
Apologies for the long silence. Last summer we started contemplating a shift toward shorter posts from more authors on a more frequent basis, and that led to a discussion of integration with social media, and pretty soon that led us to think about changing from a WordPress blog to a tumblr blog.
In the end that’s what we decided to do. Some of the static pages are still being revised, and we expect to have a Support page (that actually works!) up soon. Virtually all of the previous articles going back to 2008 can still be accessed by clicking on Archive.
Thanks to all of you who have given constructive feedback! We hope you enjoy the new us.
By Ann Gauger
Origin of life research has problems, and here’s why. DNA carries the information necessary to build proteins. It performs no chemistry and builds no cellular structures by itself. Rather, the information in DNA must be translated into proteins. But there is no direct way to convert a given DNA sequence into a protein sequence—no direct chemical association between DNA nucleotides and amino acids. Some sort of decoding mechanism is needed to translate the information encoded in DNA into protein.
That decoding mechanism involves a whole host of enzymes, RNAs and regulatory molecules, all functioning as an elegant, efficient, accurate and complicated system for copying and translating the information in DNA into a usable form. (For a comprehensive and engaging description of how information is processed in the cell, and how this process has been discovered, see Stephen C. Meyer’s Signature in the Cell [1].)
The problem is, this decoding system is self-referential and causally circular. Explaining its origin becomes a chicken and egg problem. Building the machinery that translates DNA into protein requires the prior existence of DNA, RNA and protein, all three. This should give us pause, because we have no naturalistic explanation for problems involving causal circularity.
So when it was discovered that some RNAs could carry out (very limited!) chemical reactions, scientists seeking a purely materialistic explanation for life's origin were thrilled. Perhaps here was the solution to the conundrum. Perhaps RNAs could be both catalysts and information carriers. Perhaps the first living world was RNA-based.
Fast forward to now. Researchers continue to try to design RNAs that can copy themselves, and try to expand the range of chemistries they can carry out. The RNA world, if it ever existed, though, would be a very impoverished place, based on what human designers have been able to produce so far. And the problem of how an RNA world could become a DNA/RNA/protein world would remain.
Enter the Direct RNA Templating (DRT) model of Michael Yarus et al. [2]. The hypothesis was originally based on the discovery that the activity of one RNA catalyst could be blocked by the presence of the amino acid arginine. From this result Yarus hypothesized that perhaps other RNAs would show an affinity for particular amino acids. In a series of papers he and his coworkers identified other such RNAs and, based on statistical analysis, they argued that these RNAs contained a higher than expected frequency of triplets corresponding to the particular codons or anticodons now used to specify that amino acid in the modern genetic code [3].
But is their analysis correct? In a peer-reviewed paper published this week in BIO-Complexity, Stephen C. Meyer and Paul Nelson take on the DRT model [4]. They carefully examine the claims of Yarus et al. and find them wanting. Inadequate null hypotheses, arbitrary selection of data for analysis, and unrealistic assumptions about prebiotic chemistry are just a few of the problems. Rather than go through their arguments here, I encourage you to read their paper yourself.
Why does it matter? Critics of intelligent design have advanced the DRT model as the answer to the sequencing problem—how genetic information in RNA (in the hypothetical RNA world) eventually could have been translated into more stable and versatile proteins. Based on the analysis in this paper, however, the sequencing problem has not been solved, even partially. There is no natural affinity between RNAs, amino acids, and codes. And the origin of life remains inexplicable in materialistic terms.
[1] Signature in the Cell
[2] doi:10.1126/science.3381099
[3] doi:10.1007/s00239-009-9270-1
[4] doi:10.5048/BIO-C.2011.2
By Doug Axe
Scientists employ different rhetorical strategies to accomplish different things. That shouldn’t be surprising, perhaps, but for some it is. The reason is that while the public is very familiar with rhetorical shiftiness in some occupations, they tend to see only one side of science—the confident, assertive, authoritative, we-know-what-we’re-talking-about side. Science-speak often comes across with a hint of arrogance, but since science itself depends on the goodwill of the public for its very existence, it usually corrects itself on those occasions when it oversteps its bounds.
There are a few peculiar exceptions though, where what amounts to little more than propaganda is excused in the name of academic freedom. It’s regrettable, but it happens, and the guilty institutions become known for it.
Since Oxford University is one of them (as evidenced by the fact that I don’t need to name anyone), there is particular satisfaction in bringing to light some of the hidden rhetoric from that institution. Please don’t misunderstand me. I’m not suggesting that anything that follows is in any way secretive. I’m simply suggesting that some needs—like getting grants and hiring people to work under those grants—call for a frank statement of what isn’t known, whereas the messages intended for the general public tend to emphasize or even exaggerate what is known.
But enough of my rhetoric. I’ll let this refreshing new flavor of Oxford rhetoric speak for itself. What follows is a collection of excerpts (emphasis added) lifted from a recent job description from St John’s College at Oxford University [1], prefaced with this quote from Darwin’s autobiography [2]:
During the three years which I spent at Cambridge my time was wasted, as far as the academical studies were concerned, as completely as at Edinburgh and at school. I attempted mathematics, and even went during the summer of 1828 with a private tutor (a very dull man) to Barmouth, but I got on very slowly. The work was repugnant to me, chiefly from my not being able to see any meaning in the early steps in algebra. This impatience was very foolish, and in after years I have deeply regretted that I did not proceed far enough at least to understand something of the great leading principles of mathematics; for men thus endowed seem to have an extra sense. But I do not believe that I should ever have succeeded beyond a very low grade.
Charles Darwin, 1876
Fast-forward 135 years to the present.
In the Oxford job description [1], under the heading Extracts from the grant application to the St John’s Research Centre, subheading Objectives:
1. To construct a mathematical framework, with appropriate theorems, to represent fully the core argument in Darwin’s Origin of Species, namely that the purely mechanical processes of inheritance and reproduction can give rise through natural selection to the appearance of design.
Under the same heading, subheading Summary:
Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. …
A further advantage [of the proposed work] is that by setting up a formal version of Darwin’s argument, it will raise the bar for those who claim to have their own understanding of Darwin: in the first place, it will need to be checked against the formal version; if it fails that test, it will still of course be possible to argue that the current formal version is incomplete or erroneous; but this will be a technical exercise that requires real intellectual work to be persuasive, for which words alone will not suffice. …
This project is in many ways a mathematical, formal version of the argument of The Selfish Gene. There, Dawkins articulates in words a unifying structure for all the central adaptive theories used by evolutionary biologists, and grounds that unifying structure in a fully logical framework. A mathematical version will provide more precision, and answer a class of objections.
Under the same heading, subheading Detailed Application:
The idea that organisms maximise their fitness as a result of natural selection is extremely important in many areas of biology. The explanatory apparatus of most whole organism, behavioural ecology, work would make no sense without it. However, the logical basis for the idea is in considerable doubt. The mainstream of mathematical population geneticists since about 1964 has emphatically rejected the claim that fitness is maximised. …
There has been essentially no formal consideration of the kind of optimisation that emerges so naturally from verbal arguments such as those of Darwin (1859) and Dawkins (1976).
In the main job description, under the heading The Deep Mathematical Theory of Selfish Genes, subheading About the project:
The concept of fitness optimization is routinely used by field biologists, and first-year biology undergraduates are frequently taught that natural selection leads to organisms that maximize their fitness. Dawkins’ The Selfish Gene (1976) promoted a conceptual integration of modern evolutionary theory in which genes are viewed as optimising agents, which is extremely influential and widespread today and encompasses inclusive fitness theory and evolutionarily stable strategies as well as general optimality ideas. However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. …
Generality is important, as a major aim [of the proposed work] is to find mathematical arguments that match Darwin’s verbal arguments in the Origin of Species, as well as Dawkins’s verbal arguments in the Selfish Gene and later works. …
Thus this highly abstract mathematical project will have significant implications at many different levels in biology. It will also be of interest to historians of science, as it will claim to show the underlying logic of Darwin’s great insight and of Dawkins’ conceptual unification.
[1] Retrieved from http://www.sjc.ox.ac.uk/3498/RA%20in%20Mathematics_FPs.pdf.download on 5 May 2011.
[2] http://darwin-online.org.uk/content/frameset?itemID=F1497&viewtype=text&pageseq=1
