Monday, July 31, 2017

New Study: Transgenerational Epigenetics Can Have a Profound Impact

The Third Rail of Evolution

In the spring of 2006 I gave a talk on the campus of Cornell University and afterwards was joined by then Cornell professors Richard Harrison and Kern Reeve for a sort of panel discussion or debate about biological evidences and origins. I presented a dozen or so interesting and important evidences that I felt needed to be recognized in any discussion of origins. The evidences falsified key predictions of evolution and so needed to be acknowledged and reckoned with, one way or another. One of the items on my list was the so-called directed adaptation mechanisms which, broadly construed, can include everything from non random, directed, mutations to transgenerational epigenetic inheritance. But I was in for a big surprise when Harrison and Reeve gave their response.

Directed adaptation is reminiscent of Lamarckism. Rather than natural selection acting over long time periods on biological variation which is random with respect to need, directed adaptation mechanisms provide rapid biological change in response to environmental challenges. Like physiological responses, directed adaptation can help an organism adjust to shifts in the environment. But those adaptations can then be inherited by later generations. Stresses which your grandparents were subjected to may be playing out in your own cells.

In the twentieth century evolutionists had strongly rejected any such capability. Lamarckism was the third rail in evolutionary circles. And for good reason, for it would falsify evolutionary theory. But empirical evidence had long since pointed toward the unthinkable, and by the twenty first century the evidence was rapidly mounting.

While there was of course still much to learn in 2006 about directed adaptation (as there still is today for that matter), it could no longer be denied, and needed to be addressed. At least, that is what I thought.

I was shocked when Harrison and Reeve flatly denied the whole story. Rick waved it off as nothing more than some overblown and essentially discredited work done by Barry Hall and John Cairns, back in the 1970s and 80s (for example here).

But there was a body of work that had gone far beyond the work of Hall and Cairns. Incredulously I responded that entire books had been written on the subject. Rick was quick to respond that “entire books are written about all kinds of discredited things.”

True enough. It was me versus two professors on their home turf with a sympathetic audience, and there was no way that I was going to disabuse them of what they were convinced of.

Confirmation testing and theory-laden evidence are not merely philosophical notions. They are very real problems. I’m reminded of all this every time a new study adds yet more confirmation to the directed adaptation story, such as the recent paper out of Nicola Iovino’s lab on transgenerational epigenetic inheritance in house flies, which states:

Gametes carry parental genetic material to the next generation. Stress-induced epigenetic changes in the germ line can be inherited and can have a profound impact on offspring development.

The press release gives little indication of the controversy as it admits that these findings were once considered impossible:

It has long been thought that these epigenetic modifications never cross the border of generations. Scientists assumed that epigenetic memory accumulated throughout life is entirely cleared during the development of sperms and egg cells.

It is hard enough to see how organisms can respond intra-lifetime to environmental challenges, but how can it be inherited as well? For epigenetic changes that occur in somatic cells, that information must also enter into the germ line as well. Somehow it must be incorporated into the sperm and/or egg cells.

It is an enormous problem to explain how such capabilities evolved. Not only are a large number of mutations required to make this capability work, it would not be selected for until the particular environmental condition occurred. That means that, under evolution, it would be not preserved, even if it could somehow arise by chance.

Sunday, July 30, 2017

The Astonishing Examples of Repeated Evolution

Does Similarity Imply Common Ancestry?

According to evolution the species arose as a consequence of random events, such as mutations. Yet the biological world is full of repeated designs. These so-called convergences are ubiquitous. And while a fundamental tenet of evolutionary theory is that similarity implies common ancestry, convergences are similarities found in more distant species—they cannot have arisen from a common ancestor. This falsifies the fundamental tenet that similarity implies common ancestry. This tension can be further amplified by complexity and multiplicity. Similarities in different species which are highly complex can be difficult to explain how they evolved once, let alone twice in independent lineages. Add to this similarities which are found not twice, but a multiplicity of times, and you have what the press release of a new study out of Germany on the evolution of jawed vertebrates called “astonishing examples of repeated evolution.”

Sunday, July 23, 2017

Subcellular Map of the Human Proteome Reveals “Highly Complex Architecture”

A High Degree of Regulation and Control

New research is using antibodies to map out the spatio-temporal locations of 12,003 different proteins in human cells. The results are another example of how, as Bruce Alberts put it in 1998: “We have always underestimated cells.” Alberts explained how cells were once naively viewed as something of a random affair, where molecules “were thought to diffuse freely, randomly colliding.” The new research reveals the “the highly complex architecture of the human cell” and adds more detail to the fact that the workings of the cell are far from random:

A total of 12,003 proteins targeted by 13,993 antibodies were classified into one or several of 30 cellular compartments and substructures, altogether defining the proteomes of 13 major organelles.

Although evolutionists “thought the cell was so simple,” this research is showing that the “cellular proteome is compartmentalized and spatiotemporally regulated to a high degree.” In fact “[m]ore than half of these 12,003 proteins localize in more than one compartment at the same time.” This is consistent with the fact that most proteins are capable of performing multiple functions, and is another indicator of high complexity:

Moreover, proteins that localize to more than one compartment may have context-specific functions, increasing the functionality of the proteome. The fact that proteins “moonlight” in different parts of the cell is now well accepted. … The more complex a system is, the greater the number of parts that must be sustained in their proper place, and the lesser the tolerance for errors; therefore, a high degree of regulation and control is required.

Indeed, the degree of regulation and control required for this system is not only enormous, but contrary to evolutionary expectations.

Saturday, July 22, 2017

Human Evolution: Missing Link Still Missing

The Need For Theory Evaluation

The evolution of humans is, in many ways, similar to evolutionary theory on the whole. As Colin Barras reveals in his recent article at the BBC, There are conflicting evidences, a lack of details, opposing hypotheses held with great confidence, and a wide range of explanatory mechanisms that are routinely used as needed. That much is obvious. What is a bit more subtle, and arguably even more important, is the absence of a serious evaluation of the theories at hand.

Barras’ article is a good summary, from TH Huxley and Darwin up to today, of how evolutionists have viewed human evolution. What is humanity’s phylogenetic neighbor, our so-called sister species, and what is our most recent common ancestor?

Following Huxley, gorillas or chimpanzees were typically held by early evolutionists as both our sister species and representative of the common ancestor, which swung from branch to branch and rambled along on all fours. But some evolutionists held that monkey’s were our closest evolutionary neighbor.

With the rise of molecular biology came genetic comparisons and the firm conclusion that chimpanzees and bonobos are our sister species. Huxley, it seemed, was right. Students were told, in no uncertain terms, that the chimp was our sister species—after all, we shared something like 99% of our DNA in common.

But then new evidences arose, questioning this seemingly incontrovertible truth. Subtle differences between gorillas and chimps suggested independent evolution, rather than inheritance via a common ancestor, of certain traits. Furthermore, a new fossil species, Ardipithecus ramidus, as well as anatomical and behavioral comparisons, called into question the accepted human-chimp relationship.

All of this leaves evolutionists today contemplating a range of explanations for human evolution. One common theme of all the different explanations, however, is their lack of detail. The explanations do not provide any sort of detailed account of the rise of the many unique traits and capabilities in humans.

And where detailed evidence does exist, such as in the chimp, gorilla, and human DNA data, it makes little sense (see here, here, and here, for example).

The theoretical problems and lack of detail with human evolution, and evolution in general, raise the question of how good these theories are. Evolutionists repeatedly state that evolution is a fact, just as much as gravity, heliocentrism, and the roundness of the Earth are facts. There is no question about it.

But the science does not support this claim. What we need is a legitimate, serious evaluation of the theories at hand.