Category Archives: history of biology

Lamarck and Giraffes!: Closing the Circle

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You're going to think I'm nuts but this is too good to pass up!

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One pre-Darwinian theory of evolution is credited to Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck (1744 – 1829). One component of his theory was "L'influence des circonstances" (the influence of circumstances) which we take today as an acquired trait (not a genetic trait), like bigger muscles, etc., that is a response to an environmental factor and is transmitted from parents to offspring. This (the transmission of environmentally influenced acquired traits) is referred to as Lamarckism or Lamarckian evolution.

A common example used in textbooks to illustrate this is the length of giraffe's necks. Giraffe's were originally short necked but each generation the adult giraffes would stretch their necks to reach higher leaves that were left behind. Stretching their necks resulted in the adult's neck being slightly longer (than if it had not stretched). Importantly, according to the theory, this trait, longer necks, was transmitted to the giraffe's offspring. Over many generations the necks grew increasingly longer. In Lamarck's view interaction with the environment (circumstance) led to an inherited physical change in the organism.

Okay, so with the modern synthesis of evolution incorporating Darwinian adaptation and Mendelian inheritance, among other things, we can comfortably laugh at this scenario.* However, in recent decades the role of epigenetic inheritance has been increasingly understood. With epigenetics there are not changes to a DNA sequence (mutations as we generally understand them) but "tags" are added to the DNA sequence that alters the expression of a gene. Importantly, factors in the environment the organism is exposed to change how these tags are added and this can be inherited across generations. So, there is a way for an organism's environment to influence inherited physical changes in an organism's future descendants.

A famous example is "agouti" coat color in mice. Mice that are heterozygous for an A[vy] allele have variable phenotypes ranging from yellow to brown, as a result of the influence of environmental effects.

bpa

Interestingly, when parents are exposed to compounds like Bisphenol-A (BPA) this can cause a trans-generational shift towards more yellow descendants. On the other hand when the parents diets are supplemented with large amounts of folic acid, vitamin B12, or zinc there is a trans-generational shift towards more brown ("pseudo-agouti") descendants. This has been determined to be because of differences in methylation (one form of the DNA "tags") of a promoter region of the Agouti gene sequence.

agoutimethcpg2

There are many more examples of epigenetic effects for a range of traits in a range of species. I am not going to attempt to review them here, but this is an active and interesting area of research and we are just beginning to understand how extensive this might be and the role it might play in, for example, human genetics (think for a moment of all the vitamins and chemicals you are exposed to and what effects this might have on your children and grand-children...).

Wiki_Bisulfite_sequencing_Figure_1_small

How do you detect epigenetic tags on a DNA sequence? One method is to treat the DNA with bisulfite first before amplifying and sequencing it. Bisulfite converts cytosine to what ends up appearing as a thymine (a C (to a U) to a T in the DNA sequence) but it does not affect cytosines with a methyl group that is attached. (To be clear there are more types of epigenetic "tags" then methylated cytosine, and not all types of epigenetics modify DNA nucleotides; this is just one type.)  So, you can compare bisulfite treated and non-treated DNA sequences and work out if there is a difference in epigenetic modifications.

Okapi2

Okay, bear with me. Recently the giraffe genome was reported in a comparative genomics project that included its shorter necked cousin the okapi (http://www.nature.com/ncomms/2016/160517/ncomms11519/full/ncomms11519.html). A number of genes with changes that likely lead to the giraffe's unique development were identified including FGF growth factors and HOX genes that guide development. Furthermore, the authors found changes in genes that are likely involved in tolerating toxins in their diet (acacia leaves for example are very toxic and contain a range of alkaloids).

Okay, you can guess where I'm going with this.  Giraffes eat food that is very biologically active and toxic to many other species...  Just for fun, are there epigenetic signals in the genes implicated to be responsible for a giraffe's long neck? Do these vary among giraffes? Are they correlated with neck size and/or diet? Does the signal transmit across generations?   (Could epigenetic potential have evolved to be sensitive to, and respond to, trees of different heights in the giraffe's (ancestor's) diet?)  It would be fairly straightforward to work the first part of this out using giraffe DNA samples and bisulfite sequencing. Giraffe's already serve as excellent examples of the process of evolution (perhaps most famously the route of the recurrent laryngeal nerve in giraffes). We now have the tools to determine if, after all of these years (centuries), there could also in fact be a Lamarckian "L'influence des circonstances" in giraffe neck length?

  • However, to say that Lamarck was at a conceptual dead end and only known for the theory of inheritance of acquired characteristics is a part of the general misunderstanding that is associated with the man. He was a French naturalist that was involved in a wide range of scientific topics. Lamarck rebelled against the predominant thought of uniformitarianism in nature at the time. His idea around 1800 that some aspects of nature were mutable and could change was revolutionary and formed part of the foundation for Darwin's theory of natural selection and other components of the theory of evolution.

Further reading

Agaba, M., Ishengoma, E., Miller, W. C., McGrath, B. C., Hudson, C. N., Reina, O. C. B., ... & Praul, C. A. (2016). Giraffe genome sequence reveals clues to its unique morphology and physiology. Nature Communications, 7.
 Here is  nice news report of the work: http://phys.org/news/2016-05-giraffe-neck-clues-revealed-genome.html
Feil, R., & Fraga, M. F. (2012). Epigenetics and the environment: emerging patterns and implications. Nature Reviews Genetics, 13(2), 97-109.
Gillispie, C. C. (1958). Lamarck and Darwin in the History of Science. American Scientist, 46(4), 388-409.

Nothing in biology makes sense...or does it?

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Theodosius Dobzhansky (1900-1975) was a very influential geneticist and one of the architects of the modern synthesis of genetics and evolutionary biology; I heard that he also liked to make French-toast for breakfast.  He is in my academic lineage as my Ph.D. advisor's advisor's advisor's advisor---sort of my academic great-great-grandfather.

There is a famous essay he wrote in 1973 that is widely quoted and referenced; "Nothing in Biology Makes Sense Except in the Light of Evolution" (The American Biology Teacher 35:125-129).  This is repeated over and over in the literature, grant applications, department and lab websites, and class teaching materials, etc., dare I say it, ad nauseum (e.g., Varki, A. (2006). Nothing in glycobiology makes sense, except in the light of evolution. Cell, 126(5), 841-845; Valas, R. E., Yang, S., & Bourne, P. E. (2009). Nothing about protein structure classification makes sense except in the light of evolution. Current Opinion in Structural Biology, 19(3), 329-334; Seyfried, T. N. (2012). Nothing in cancer biology makes sense except in the light of evolution. Cancer as a Metabolic Disease: On the Origin, Management and Prevention of Cancer, 261-275).

However, there is odd and little known historical detail behind this that Fred Gould (NCSU) pointed out to me in a conversation we had last year.  Almost 10 years before, in 1964, Dobzhansky published an address entitled "Biology, Molecular and Organismic" (American Zoologist 4:443-452).  If you scan through it there is a familiar line in an unfamiliar context (p. 449) "I venture another, and perhaps equally reckless, generalization---nothing makes sense in biology except in the light of evolution."  To put this into perspective, in the article he is arguing against a reductionist hierarchy in science, "the proposition that chemistry and physics are sciences more 'advanced'" and that "the aim of biology is, then, to describe life in terms of first of chemistry, and eventually of physics."  Dobzhansky goes on to argue that biology should proceed on two fronts, one a mechanistic reductionism and another that studies higher order emergent properties of the evolutionary process.  "Both the mechanistic and evolutionary explanations are pertinent to, and are made use of, in molecular as well as in organismic biology. These explanations are not alternative or competing; they are complementary, without, however, being either deducible from or reducible to each other. ... To treat molecular biology instead as a bludgeon with which to destroy, or to reduce to insignificance, the organismic biology is to basically misunderstand the nature of life."

So, Dobzhansky first made the statement "nothing makes sense in biology except in the light of evolution" as an example of an argumentum ad absurdum, a ridiculous extreme that was not true.  Rather, he seemed to intend that not everything in biology makes sense when only considering evolution or molecular biology independently; they must be both considered together for a more realistic understanding of biology.  Evolution does not do a good job of explaining hydrogen bonding between two DNA strands, chemistry does; yet, this understanding is needed to work with DNA in the lab and better understand how genetic inheritance works, which is squarely biological.  Conversely, neither chemistry nor physics can even begin to explain why we have nonfunctional remnants of a gene (GULO, a.k.a, GLO and GULOP in humans) involved in vitamin C synthesis on our eighth chromosome (e.g., Drouin, G., Godin, J. R., & Pagé, B. (2011). The genetics of vitamin C loss in vertebrates. Current Genomics, 12(5), 371; Helliwell, K. E., Wheeler, G. L., & Smith, A. G. (2013). Widespread decay of vitamin-related pathways: coincidence or consequence? Trends in Genetics, 29(8), 469-478).  Chemistry and physics tells us it is there, but how did it get there?  Neither one nor the other views are complete.  Biological evolution proceeds with what it has to work with, including the opportunities and constraints provided and imposed by chemistry and physics as well as other aspects of biology itself (such as existing gene interactions, behavior, and anatomical patterns---famous examples being the panda's "thumb," and the giraffe's recurrent laryngeal nerve).

In this light it is odd that Dobzhansky then used the statement as the title of his 1973 essay, without the balanced arguments made earlier.  The line then became famous and his earlier address faded into obscurity.  I guess it goes to show that to be successful it often pays to make an extreme and simple statement rather than a more accurate and complete statement.  "Nothing succeeds like success" (Dobzhansky 1964).