Supplemental Text

Putting Genes in Perspective

Stephen L. Talbott

This article is supplemental to “Genes and the Central Fallacy of Evolutionary Theory”, and can best be read in conjunction with that essay. Both pieces are part of a larger work in progress entitled: Toward a Biology Worthy of Life. Original publication of this article: February 28, 2013. Date of last revision: March 24, 2013. Copyright 2013 The Nature Institute. All rights reserved.

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There are many phenomena showing how the organism contextualizes its DNA in an active, directed, and stable manner. The DNA, like all parts of the cell — and like all parts of the organism as a whole — is subordinated to larger purposes. Here I can mention only a few examples in passing.

Environmental influences. Among honey bees, the queen and workers typically have the same DNA. Yet, “despite their identical clonal nature at the DNA level, workers and queens differ markedly in morphological and physiological features and have contrasting reproductive capabilities, strikingly diverse life spans, and very different behavioral repertoires” (Kucharski et al. 2008*). The differences originate chiefly in the fact that a larva destined to become a queen is fed royal jelly rather than the food given to workers.

Food is not the only environmental factor capable of contributing to major phenotypic change. The sex of offspring — for example, among some reptiles (crocodile and turtle) and birds (Australian brush-turkey) — is determined by the incubation temperature of eggs during a portion of embryonic development. So in these cases the same DNA heritage is compatible with both male and female traits, stably maintained throughout the organism’s lifetime. Likewise, temperature in combination with photoperiod plays a role in determining whether an ant larva becomes a queen.

An insect’s color may change with the seasons. This is often described as a method of camouflage, but it also affects other things such as heat retention. Many birds change color with the seasons, and so do some mammals such as the arctic fox.

The presence or absence of predators, signaled by emitted chemicals, may result in physiological changes in their prey. For example, if a water flea (or its mother) lives in the presence of certain predacious fly larvae, the flea will develop a large, protective “helmet”. In the absence of predators, the head is smaller, allowing the flea to move more agilely in pursuit of its own food.

Finally — and returning for a moment to those honeybees — the worker caste is not uniform. Workers begin as nurses for larvae and later become foragers in the field. The two subcastes differ both bodily and behaviorally, with the foragers, for example (but not the nurses) engaging in the well-known “bee dance”. It has now been shown that if you remove nurses from the hive, foragers recognize the situation and some of them revert to being nurses. Part of what happens in this reversion is epigenetic: for example, the organism orchestrates changes to DNA methylation in the brain — a process, of course, that leaves the bare DNA sequence (as usually conceived) unchanged. Some of this methylation results in repressed or otherwise altered gene expression — especially of regulatory genes — and some of it leads to revisions in mRNA splicing. Both sorts of change have ramifications throughout the cell and organism (Herb et al. 2012*).

Cancer and context. Cancer often involves DNA mutations, epigenetic changes, rapid proliferation of tumor cells, metastasis (migration of cancerous cells to a new location in the body), and the loss of normal form. The organism, you might say, loses its ability to discipline its parts in relation to the proper form of the whole.

A number of researchers have investigated what happens when cancerous cells derived from a particular cell type are placed in a young embryo at the proper location for that cell type. The results can be remarkable. For example, metastatic melanoma cells inserted into a chick embryo failed to develop tumors. Instead, some of the diseased cells responded to chick embryonic environmental cues, forming normalized tissues (Kulesa et al. 2006*) — this despite the fact that the “cancerous” mutations presumably remained. So whereas we spoke in the main article of differentiated cell types containing the same DNA, here we see the establishment of a common cell type despite differences in DNA.

In a similar vein, it was shown many years ago that a salamander limb with an induced tumor could be amputated through the middle of the tumor, in which case the regenerated limb tissues extending from the remaining half of the tumor were normal (Rose and Wallingford 1948*). Referring to this work, Michael Levin, director of the Center for Regenerative and Developmental Biology at Tufts University, remarks on “the importance of large-scale patterning mechanisms to what is often thought of as a cellular- or gene-level process”. Like an embryo, the area of regeneration in the limb of a salamander is a locus where strong formative influences come to bear.

Speaking of regeneration (and development) in general, Levin goes on to say that “regeneration ceases when precisely the right size structure has been rebuilt, indicating a coordination of local growth with the size and scale of the host”. However, it’s not just a matter of attaining the correct size:

Consider what happens when an amphibian tail blastema [a group of cells capable of growing into an organ or body part] is grafted to the side of a host animal. A tail results at first; however, over the subsequent few months, this tail is reshaped into a limb, illustrating that the control of local regions’ fate is integrated into the large-scale morphology appropriate to the host animal even if their structure has to be remodeled. (Levin 2011*)

Working from a different angle, researchers at the University of California, Berkeley, and the Lawrence Berkeley National Laboratory found that, when they applied physical compression to breast cancer cells, the cells reverted to a non-cancerous phenotype, despite the continuing presence of the supposedly causal genetic mutations (Yang 2012*). The study results, reported at the December, 2012 annual meeting of the American Society for Cell Biology in San Francisco, also showed that, after receiving the compression stimulus, the cancerous cells resumed the peculiar rotational movement of normal cells as they form organized, milk-secreting structures. Cancerous cells, by contrast, do not rotate coherently.

Cancer cells are thought to have a lot in common with stem cells. An American and Australian research team found that heterogeneity and plasticity of stem-cell populations “are modulated by extrinsic signaling”. An emerging view of the stem-cell state “holds that it is not an invariant and cell-autonomous state but, instead, should be considered as the dynamic response of the cell lineage as a whole to the external environment” (Pera and Tam 2010*).

And how could cell populations in a developing organism not be modulated by the wider environment? The establishment or maintenance of proper form could never be anything other than contextual, governed from above downward, since form itself — living form — is a patterning of relationships, which is much the same as saying it is a patterning of contexts. This patterning — as a distinctive shaping and adaptive way of being, not as any sort of fixity — remains consistent even in the face of disturbances, so far as circumstances allow, and the qualitative goal is achieved through the coordinated activity of a whole.

None of this can be merely incidental to genetic “instructions”. Rather, it is a living capacity to bend and subordinate the genome to the requirements of the organism.

Nucleus versus cytoplasm. There is a long history of debate concerning the relative roles played in development and inheritance by the DNA-containing nucleus and the cellular cytoplasm (Sapp 1987*). Throughout most of the past century, and especially during the era of the double helix and molecular biology, the nucleus has been seen as supremely dominant.

However, certain threads of research have suggested that this view is imbalanced, and the recent prominence of cloning and stem cell research have dramatically signaled this imbalance. In one method of cloning, a fully differentiated somatic cell nucleus is inserted into an egg cell from which the nucleus has been removed. (This is what was done in 1996 with the celebrated sheep, Dolly.) The egg cytoplasm “reprograms” (as the prevailing jargon has it) the differentiated nucleus so that it reverts to something like the pluripotency of a zygotic nucleus.

See also the supplemental text, “The Seat of Power: Nucleus or Cytoplasm?”

There is also the phenomenon of induced pluripotency whereby (to take one example of it), a particular set of protein transcription factors is injected into a more or less differentiated cell, and the cell begins to take on a stem-cell-like or pluripotent character.

In all this we see a kind of artificially induced reversal of the normal process of differentiation. The cell still governs its DNA, but now in dedifferentiation.

Epigenetics and the inheritance of acquired characters. There has been a slow but steady increase in the documented cases of so-called Lamarckian inheritance, in which an acquired trait of an organism, unrelated to any change in the DNA sequence, is inherited across successive generations. The main focus of interest has been on epigenetically mediated inheritance — primarily stemming from DNA methylation (the attachment of methyl groups to particular “letters” of the DNA sequence), and histone modifications (chemical changes in certain proteins closely bound up with DNA). But other factors are now coming to the fore, including diffusible molecules such as RNA and protein (which are transmitted through the germ cells) and, more broadly, anything that may affect the dynamics of chromosome interaction in the nucleus.

Inherited effects of the relevant sort, when transmitted via the gametes, can not only pass down through multiple generations, but do so without any necessity for repetition of the conditions originally precipitating the trait at issue. Often the transmission occurs through the female line (unsurprisingly, since the female egg contains a great mass of substance in addition to DNA), but instances of transmission through the male line are now being found as well (Carone et al. 2010*; Yazbek et al. 2010*).

Among the more frequently cited examples of transgenerational epigenetic inheritance: various dietary effects of an ancestor upon subsequent generations have been noted, and female rats exposed to a fungicide during pregnancy produce male offspring with abnormal sperm production. The latter trait is subsequently inherited through the male line, and apparently involves epigenetic and genetic changes. Also, a study of the fruit fly showed that heat stress-induced changes in eye color could be inherited by subsequent generations independently of DNA sequence changes. (See Daxinger and Whitelaw 2012* for a review.)

While such phenomena do indeed help to show that more or less stable features can be inherited independently of changes in the DNA sequence, they are not my main concern here. That’s because — as discussed in the main article — the nature of an organism’s activity is more fundamental to its functioning, including its heritable bequest, than any well-defined and fixed traits or configurations of substance.

Here’s one way to look at what’s been happening. Their curiosity about how genes “explain” the organism has led researchers outward from the supposed genetic core of explanation to what is often considered a separate “layer” of “encoded information — the epigenetic layer. The problem they find with this layer as a bearer of inheritance is that it is not strictly encoded at all, being more fluid and less well defined than the DNA sequence. And it is interwoven with many dynamic and difficult-to-track processes in the cell.

But, in reality, that’s exactly what points us in the right direction. Instead of trying to discover a fixed epigenetic code” and evidence for unchanging, transgenerational effects of epigenetic marks, researchers should realize that the study of this new layer of regulation is inseparable from yet other layers playing upon one another and all coming together in a grand symphony of meaningful interaction. In other words, backing away from DNA to look at some of the processes directly impinging upon it is a good first step. But it is only a first step, and the vertigo we may experience at discovering the “instability”, contextual responsiveness, and dynamism of epigenetic processes may prove a valuable training. A training, that is, in recognizing the far more extensive movements and exchanges testifying to the organism’s overall intentions in being this kind of organism and in providing for itself a fully functioning heir of its own kind.

References

Carone, Benjamin R., L. Fauquier, N. Habib et al. (2010). “Paternally Induced Transgenerational Environmental Reprogramming of Metabolic Gene Expression in Mammals”, Cell vol. 143 (Dec. 23), pp. 1084-96. doi:10.1016/j.cell.2010.12.008

Daxinger, Lucia and Emma Whitelaw (2012). “Understanding Transgenerational Epigenetic Inheritance via the Gametes in Mammals”, Nature Reviews Genetics vol. 13 (March), pp. 153-62. doi:10.1038/nrg3188

Herb, Brian R., Florian Wolschin, Kasper D. Hansen et al. (2012). “Reversible Switching between Epigenetic States in Honeybee Behavioral Subcastes”, Nature Neuroscience (advance online publication: Sep. 16), doi:10.1038/nn.3218

Kucharski, R., J. Maleszka, S. Foret, and R. Maleszka (2008). “Nutritional Control of Reproductive Status in Honeybees via DNA Methylation”, Science vol. 319 (March 28), pp. 1827-30. doi:10.1126/science.1153069

Kulesa, Paul M., Jennifer C. Kasemeier-Kulesa, Jessica M. Teddy et al. (2006). “Reprogramming Metastatic Melanoma Cells to Assume a Neural Crest Cell-like Phenotype in an Embryonic Microenvironment”, PNAS vol. 103, no. 10, pp. 3752-7. doi:10.1073/pnas.0506977103

Levin, Michael (2011). “The Wisdom of the Body: Future Techniques and Approaches to Morphogenetic Fields in Regenerative Medicine, Developmental Biology and Cancer”, Regenerative Medicine vol. 6, no. 6 (Nov.), pp. 667-73. doi:10.2217/RME.11.69

Pera, Martin F. and Patrick P. L. Tam (2010). “Extrinsic Regulation of Pluripotent Stem Cells”, Nature vol. 465 (June 10), pp. 713-20. doi:10.1038/nature09228

Rose, S. Meryl and Hope M. Wallingford (1948). “Transformation of Renal Tumors of Frogs to Normal Tissues in Regenerating Limbs of Salamanders”, Science vol. 107, p. 457.

Sapp, Jan (1987). Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics. Oxford: Oxford University Press.

Yang, Sarah (2012a). “To Revert Breast Cancer Cells, Give them a Squeeze”, UC Berkeley News Center. Retrieved from http://newscenter.berkeley.edu/2012/12/17/malignant-breast-cells-grow-normally-when-compressed/.

Yazbek, Soha N., Sabrina H. Spiezio, Joseph H. Nadeau and David A. Buchner (2010). “Ancestral Paternal Genotype Controls Body Weight and Food Intake for Multiple Generations”, Human Molecular Genetics vol. 19, no. 21, pp. 4134-4. doi:10.1093/hmg/ddq332

This document: http://natureinstitute.org/txt/st/mqual/genome_10_genocentrism.htm.

Steve Talbott :: Putting Genes in Perspective