lunes, 24 de marzo de 2014

A Challenge to the Supremacy of DNA as the Genetic Material


About a month ago, a news release stood out among the many I get every day: “A challenge to the genetic interpretation of biology,” from a physicist and chemist from Finland, Arto Annila and Keith Baverstock. They’d just published “Genes without prominence: a reappraisal of the foundations of biology,” in the Journal of the Royal Society Interface.

One sentence from the news release grabbed me: “The result is evolution from simpler to more complex and diverse organisms in both form and function, without the need to invoke genes.Instead, Drs. Annila and Baverstock invoke thermodynamics.

I was mesmerized, mostly because I am immersed in writing the 11th edition of my human genetics textbook and a non-DNA-centric view got me thinking. So I read the paper and asked the authors to guest post. Their idea brought me back to pre-1953 thinking that proteins are the genetic material, mostly because we knew more about them than the mysterious goop on soiled bandages that was DNA.

Then last week I posted here about the information from a dozen sequenced human genomes not being all that clinically useful, at the same time that the blogosphere trumpeted the not-very-surprising finding that a gene attached to obesity was actually controlled by another gene. The news last week seemed to validate Drs. Annila and Baverstock’s concern about genome sequencing entering the clinic when we don’t fully understand how genes interact at the level of their products, the proteins.

Dr. Baverstock kindly agreed to post. His impressive bio is here. Most notably, he brought to global attention the increased childhood thyroid cancer incidence in Belarus caused by radioactive iodine from the Chernobyl accident. (I had thyroid cancer although I’ve never been near a leaking reactor.) Here he shares his thoughts, lightly edited, subheads added:

A VIEW FROM PHYSICS
Arto Annila and I are making the seemingly outrageous claim that mainstream biology, since around the 1920s, has pursued a course that is deeply flawed. Critical to that course is the notion that genes are Mendel’s units of inheritance and that their material realization is a DNA base sequence. We propose instead that Mendel’s unit of inheritance is a process involving the interaction of mainly activated proteins contributing to an attractor state that represents the phenotype. Many will find this language of physics unfamiliar. However, cells are complex dissipative systems (CDS) in that they consume energy and thus operate according to the 2nd law of thermodynamics as it applies to open systems.
A lily cell dividing. (Andrew S. Bajer)
First, two irrefutable facts in justification of our position:
  1. When cells divide they inherit the state of the cell. If this were not the case, cancer and differentiation would have to be one-step processes. The state of the cell cannot be encoded on the DNA base sequence: it is the active proteome.
  2. Key biological processes, such as development, growth and aging, are irreversible in time, whereas standard textbook physics describes time reversible deterministic dynamics.
It is very well known that at cell division the cytoplasm is partitioned between the two progeny, but not emphasized, as we propose, that it contains a coherent complex process of interacting proteins. When this state is understood as the unit of inheritance, the epigenetic memory that enables processes, like differentiation, to take place over several cell generations is a natural manifestation. In addition, CDS physics supports the phenomenon of quasi-stability – that is, stability within limits: attractors are quasi-stable states formed by the interacting proteins. This would mean that inheritance at the cellular level is not after all a matter for the nucleus, but rather for the cytoplasm.

NOT JUST THE NUCLEUS
The nucleus/cytoplasm issue was hotly debated around the turn of the century – not the last one but the one before, and eventually resolved in favor of the nucleus by the geneticist T H Morgan in 1926. It’s clear that components of the egg cytoplasm are inherited at fusion, the mitochondria for example, but it has generally been regarded that the sperm delivers only genomic DNA. However, studies on male fertility have revealed that proteins essential for successful fertilization are present in the sperm and some of the chromatin is in a non-condensed state and thus, possibly even active. Therefore, we can assume that the sperm is capable of supporting a protein-based attractor state.


One experimental way to resolve the nucleus/cytoplasm issue is cross species nuclear transfer to enucleated eggs. This has not proved possible with mammals, but has been successful with fish. Enucleated goldfish eggs transplanted with nuclei from carp eggs develop with the outward appearance of the donor carp, but with a vertebral number (26 to 31) consistent with goldfish (26 to 28) rather than the genomic DNA donor carp (33 to 36). We assume that when two dynamic attractors are placed in a common environment, as in the case of the zygote, that they will “synchronize” as, for example, with Huygens’ clocks. Therefore, we argue that biology can explain inheritance on the basis of a sound foundation in the appropriate physics, without resorting to mechanistic narratives involving genes.

Furthermore, work in the 1970s demonstrated that enucleated HPRT-competent (HPRT is an enzyme whose absence causes the awful Lesch-Nyhan syndrome, an inborn error of metabolism-RL) fibroblasts in vitro could correct HPRT deficiency in fibroblasts with an intact nucleus, by transferring molecules via gap junctions, without the need for protein synthesis. In addition, erythrocytes (red blood cells) dispose of their nuclei at the last stage of differentiation, but retain, for example, the circadian rhythm function for their lifetime.

In fact, the evidence clearly points to routine cellular function (apart from cell division) and regulation in somatic cells being a matter for proteins without the intervention of genes. If, for example, the dark/light rhythm changes (travel over a few time zones) then intervention involving new transcription to adjust the circadian rhythm does occur, but otherwise circadian rhythm is taken care of by protein chemistry, as has been demonstrated in vitro.

DID MENDEL PICK CHERRIES, NOT PEAS?
If you have read as far as this, you are no doubt wondering about the plethora of experimental evidence for the action of genes that has accrued since Mendel experimented with pea plants in the monastery garden in the mid 1800s. It is impressive, but how complete is it and what does it really explain?

The American geneticist Richard Lewontin drew attention in 1974, in a book on population genetics, to the fact that all experimental geneticists since Mendel had studied very marked, i.e., easily measured, traits, such as flower color. He identified the following paradox “what is measurable is not interesting and what is interesting is not measurable.” We suggest that these marked traits are rather special and they often do associate with gene sequences, but the association is not causal. A correlation or association as such does not reveal driving forces of ensuing effects. Key here is the thorny issue of protein folding.

THE IMPORTANCE OF PROTEIN FOLDING
An important step in the Central Dogma (DNA encodes RNA encodes protein-RL) is the folding of the peptide to form the protein, which can become biologically activated and contribute, as a component of the attractor, to phenotype.

Anfinsen’s dogma, derived from experiments with the enzyme ribonuclease, says that the amino acid sequence of the peptide dictates the folding. Were that true the “protein folding problem” would have been understood by now. In fact, predicting the folded structure is still an unsolved problem and according to Arto Annila that is because the folding process is a dissipative (energy consuming) non-determinate process. It is non-determinate because of the involvement of the environment in which the folding takes place.

An extreme example is the involvement of chaperone proteins, which provide an environment favoring a specific folding. Therefore, we have the possibility that a single amino acid sequence, as a peptide, dictated by a gene coding sequence, can fold into more than one protein and therefore perform more than one biological activity: the determinate relationship between sequence and biological function, crucial to the Central Dogma, is violated. It is, of course, also violated by the several ways in which a single multi-exon gene sequence can be spliced to produce several peptides.

EMERGENT PROPERTIES
Another aspect of the physics of dissipative systems is the role of symmetry breaking and the consequent emergence of new properties. Symmetry breaking may sound obscure, but it is a simple concept.

Liquid water has perfect symmetry in that no matter from which direction you look at the molecules, the view is the same. A perfect sphere has perfect symmetry for the same reason. If the water freezes to ice, the perfect symmetry is lost or broken and the property of rigidity emerges. In Finland, the lakes freeze over in the winter and roads across the lakes open up, exploiting this emergent property. In this case the symmetry is broken by a phase transition, but any transfer of energy has the potential to break symmetry and therefore to give rise to emergent properties.

We see this all the time in chemistry. If we take a mixture of the harmless and odorless gases, nitrogen and hydrogen, and heat them to a high temperature, exchange of electrons between the two molecules occurs (symmetry breaking) and ammonia is the product with the emergent properties of a noxious and pungent gas. If this reaction had never been performed, there would be no way to predict, from the physical properties of hydrogen and nitrogen, the properties of ammonia – its properties are emergent.

THE PROMINENCE OF PROTEINS
What we believe drives the cell to deliver its phenotype is protein chemistrychemistry in which information derived from the folding process (not from the amino acid/DNA base sequence) is processed through the attractor to yield the very specific, but emergent, and therefore unpredictable even from knowledge of the proteins, let alone the DNA sequence, properties of the cell. So the sequence information in DNA serves only to specify the amino acid sequences of peptides; the emergent information that underpins the phenotype is not even primarily of the same type as the sequence information.

Sequence information is usually regarded as being composed of “bits,” but the emergent information carried by proteins is physical in character. Consider a notice outside a café in say Tucson, Arizona. It says, in Finnish, that anyone is welcome to visit for a free lunch on Wednesdays. The proportion of Finnish speakers eating lunch in that café on a Wednesday is likely to be far higher than that in any other café in town. The information in the notice can of course be quantified in terms of “bits,” but that is irrelevant to the “physical nature” of the information that only Finnish speakers recognize. Enzymes express their activity by their ability to recognize a specific substrate with which they can react and we are suggesting that this kind of physical recognition process underlies the interactions between cellular proteins and thus, the operation of the attractor and therefore, cellular phenotype.

The attractor is also responsible for the regulation of the cell: that is why enucleated cells retain biological functions and even communicate and initiate functional activities, such as building gap junctions or exhibiting circadian rhythm. This forces us to the conclusion that causality in cells is exercised downwardly from the phenotype to the genotype (for example, to initiate transcription or even modify the genomic sequence), exactly the reverse of the Genotype to Phenotype (G -> P) concept underpinning population genetics.

However, if we think about the origin of life from a non-creationist perspective it is difficult to see how it could have been otherwise: the life process initiated itself and recruited nucleic acids in order to retain the necessary peptides as the cell’s raw materials. Recent evidence shows that in the period from 4.5 to 3.8 billion years ago, a great deal of carbon was delivered to the Earth via meteorites and that the shock of impact was sufficient to synthesize amino acids. Meteorites are also believed to have delivered bases. From the perspective of the physics of complex dissipative systems, it was almost inevitable, given the climatic conditions on Earth, that energy from the Sun, via the second law of thermodynamics, would concoct a form of chemistry we call life.

So as astronomers discover ever-increasing numbers of planets, in and beyond our galaxy, orbiting suns in what is known as the Goldilocks zone, it seems inevitable that Earth is not alone in the Universe in supporting the phenomenon we call life. In the evolution of how we explain that phenomenon, genetics and genes have played a prominent, even dominant, role. Genetics is, however, only a statistical association between something we had to infer and something we could observe.

Now that genome sequencing is routine and we no longer have to infer the genotype, we can see things are not so simple. We are faced with either generating ever more complex genetics-based narrative explanations for biological behavior or looking for a more rational basis for biology: we opted for the latter.

ORIGINAL: PLOS
March 20, 2014

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