A critique of "The Placenta Problem: How Common Descent Fails", an article by Ann Gauger of the "Discovery Institute"

https://barryhisblog.blogspot.com/p/on-placenta-problem-how-common-descent.html

These are my comments on a blog entry in the mendaciously titled "Evolution News", an intelligent designer spotter's blog from the "Discovery Institute". 

https://evolutionnews.org/2016/06/the_placenta_pr

Why the use of scare quotes? Because the "Discovery Institute" has made no discoveries since its inception in 1991, and "Evolution News" is about attacking evolutionary science, and is very rarely news.

As we shall see, mendacity is the theme with this outfit.

But first, I shall deal with Gauger's blog page. There is some waffle, so I will cut to the relevant content. The original article is available at the link given just above.

In this blog, my notes are in red, and Gauger's material is indented and in black.  Facebook has virtually no rendering. It's barely better than teletype! That's why I post links to blog pages on Facebook.

To understand what this is about, you need to know what a placental syncytium is. Please skip this paragraph if you are already clear about this. Otherwise, don't worry. This is not highly technical, although some unfamiliar terms are being used. Try and see past the jargon. A syncytium is just a cell of the body which contains multiple cell nuclei. It is formed by the agglomeration of cells, that each, originally,  had their own single nucleus. There are different types of syncytia, but a placental syncytium forms part of the placenta in placental mammals. Simply put, they form a semi-permeable barrier between the mother and the fœtus, allowing the exchange of nutrients and waste products, and protecting the fœtus from pathogens and from potentially dangerous immune responses by the mother's body itself. 

Now an interesting fact is that certain viruses, retroviruses, of which HIV is an example, have a trick for efficiently countering the immune system. HIV counters immune system T cells by fusing them together to form a syncytium. This is done using a retroviral envelope (env) gene that allows the virus to attach to and merge with a host cell in the first place. What does this have to do with placental syncytia? Well, the genes responsible for forming placental syncytia, called syncytins, are found in endogenous retroviruses, (ERVs - see my ERV FAQ @ https://barryhisblog.blogspot.com/p/endogenous-retroviruses-frequently.html) embedded in the DNA of all placental mammals, in the same relative position, within the ERV, as you find the env gene in non-endogenous retroviruses! This is very powerful evidence for ERVs having been inherited from animals who had had a germ (egg or sperm) cell infected by a retrovirus, and so has become heritable. This, in turn is slam-dunk evidence that different 'kinds' of creatures had common ancestors. Humans and chimpanzees for example. This is the reason why evo-phobic intelligent designer spotters are so desperate to question the evidence, trying to argue that ERVs were designed into genomes. No. Envelope genes and syncytin formation is a feature of retroviruses themselves.

"Design is both explanatory and predictive, particularly when dealing with pattern breaking observations in biology, where common descent doesn’t work as an explanation."

Here, we have Gauger misrepresenting what science is saying. Mendacity. The scientific explanation of syncytia is not dependent on common descent! It is real scientists, doing real scientific work, who discovered that there are different placental syncytia in different placental lineages. Not everything in our genomes descends from common ancestors.

"Let me show you. According to the theory of common descent, all true mammals are supposed to have descended from a common ancestor with a placenta. This is a trait common to all mammals. However, it has been a puzzle for some time that placentas differ in the form they take among different mammalian clades."

Bit of a pedantic niggle here, but it does suggest that Gauger's scholarship is not what it is cracked up to be, and neither is the "Discovery Institute's" proofreading and review process. Not all "true mammals" have placentae. The non-placental mammals are the monotremes and marsupials.

And there is no puzzle. Syncytins from different ERVs are found in different lineages because they have been inherited from different retroviral infections!

"In the year 2000, French researcher Thierry Heidmann and coworkers found that genes derived from endogenous retroviruses (ERVs) appear to have been coopted to perform an essential role in placental formation. These genes, which resemble the ERV envelope gene env, make a protein that originally promoted fusion of the virus with its host cell’s membrane, but now acts to promote fusion of membranes between the embryo and the lining of the uterus. These “repurposed” proteins are called syncytins. They are essential for placental formation, yet are of independent origin in different kinds of mammals — primates have one kind, mice another, rabbits, cows, and carnivores yet others. They are clade-specific. In fact, in 2015 a functional syncytin was found in several marsupials, extending the presence and essential function of the protein to all placental mammals examined. All syncytins are lineage-specific, meaning that each mammalian clade has its own syncytin, with a unique sequence and location in the genome. They must have inserted themselves (or been placed there) after the separation of the mammals into different clades! This means there must have been multiple independent acquisitions of these syncytins to participate in an essential process that is common to all mammals. Why should there be unique syncytins in each clade?"

Unique endogenisations, of course!

"What we have to explain is the unique and independent group-specific cooption of syncytins for a function that is essential for placental development, a feature common to all mammalian groups. Six independent origins for the placenta! There is no evidence of a grand ancestral syncytin shared by all groups that was later replaced by other syncytins, so the common descent explanation of the placenta in mammals fails."

Sneaky, Ann. Nobody is arguing for the common descent of syncytins. It is possible that there was one ancestral syncytin, but that is not essentially so. And there IS evidence for a history of the co-option (exaptation) of different examples of these genes over time - examples of more than one type of syncytin in the same creatures genome, with unambiguous evidence that they were acquired at different times. See https://barryhisblog.blogspot.com/p/long-terminal-repeats-ltrs.html

"I repeat: distinct syncytins for cows, carnivores, rodents, primates, rabbits, and even tenrecs (a species thought to retain features of primitive mammals). We all recognize these clades based on their traits — cows are different from carnivores, which are different from rodents, which are different from chimpanzees. Even nursery school children can tell the difference. And they are all thought to have descended from a common ancestor, the proto-mammal. Well, apparently, these well-defined clades of mammals make their placentas using analogous but distinct proteins. This perhaps explains why the placentas of each clade differ in their structures. But it flies in the face of the idea that all mammals are descended from a single kind of ancestor with a single kind of placenta."

And here we have the central lie behind Gauger's piece. It is not a necessary prediction of evolution that all placental mammals descend from "a single kind of ancestor with a single kind of placenta". It is real scientists, doing real science, who have discovered that the different syncytin genes are present in different lineages.

"I’ll quote a review paper on syncytins. These are the people who discovered syncytins, and they have done great work. Yet they are forced into a corner by their own work and the idea of common descent."

… syncytins are ‘new’ genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell-cell fusion of syncytial cell layers at the fetal-maternal interface. These genes of exogenous origin, acquired ‘by chance’ and yet still ‘necessary’ to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.

"Rather than postulating six independent, random capture events in placental development, they are now postulating at least one more, a founding syncytin leading to a primitive placenta, then the other syncytins to replace that one in each lineage. Each replacement must have had a clear selective advantage as time went on to make the replacement possible, and each must be the outcome of a random series of events. To say it again, the common descent prediction is that there must have been a founding syncytin in the first mammal with a placenta, or something else that functioned in syncytin’s place, in order for the primitive placenta to arise and subsequently be passed to all mammalian clades. For which there is no evidence, and may never be."

Repeating a lie does not make it the truth, Anne. And your prejudices are interfering with your reading comprehension. "...may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene". "May", not "must". And so what if we suppose that there was single common ancestral syncytin that has been replaced but is no longer identifiable? How does this argue against common ancestry and the exaptation of retroviral env genes? 

"Can common descent explain the unexpected observation of six independent origins for the placenta? No. Could it predict it? No."

"Common design has an explanation, but not one that will be palatable to my interlocutors. The designer used the same idea six different times to produce the same outcome in six different “designs” (clades). That’s another way of saying all these clades have the same outcome, the placenta, but achieved by independent uses of the same idea."

Update - a comment from a reader of this artice: "ID is compatible with one env gene. It is compatible with half a dozen different env genes. It is compatible with each species having its own unique env gene. It is compatible with penguins having placentae. It is compatible with bats having feathers. It is compatible with human beings having a unique genetic code not shared with any other organism. It is compatible with every species of organism having a unique genetic code.

It is compatible with literally every conceivable observation, even impossible ones.

Ann might think this is a strength of her "theory." No actual scientist does." - Eric Murphy commenting on the Facebook group, Intelligent Design - Is it Science? 
https://www.facebook.com/groups/424005034433466/posts/2549300081903940/

"Convergent design is to be expected under the design hypothesis because the designer is not constrained by an evolutionary tree. He can reuse ideas that work in one setting in a different place. In fact, he can mix and match his methods to get to any outcome he wants. I am thinking of echinoderms (sea stars and sea urchins) that look alike as adults but get there by very different developmental paths, or two very different animal groups that come up with similar molecular solutions to create a new function, echolocation."

Whatever happened to the creationist bleat, "same design, same designer"? Here is a list of questions that anyone arguing that ERVs were designed should be able to answer. A few have tried, but without any success. Here is your chance, Ann, to shine as a leading light of intelligent designer spotting. https://barryhisblog.blogspot.com/p/in-science-we-apply-principle-of.html 

"Convergent design is clearly observable across biology but has no evolutionary mechanism. There are proposed reasons for it but no demonstration. I can hear in my head the arguments of evolutionary biologists: intrinsic constraints, canalization, living in similar environments or ecological niches, you have no demonstration either…"

The evolutionary mechanism is that common problems and challenges are met, independently, with similar solutions. Think of fishes, cetaceans and ichthyosaurs. That body shape is the optimal one for movement through the water, and nobody but a creationist or an intelligent designer spotter questions why.

"So then maybe the answer comes down to probability."

"In considering these alternative explanations, ask yourself, how likely is it that a retrovirus would infect, invade the germ line (the cells that make eggs and sperm), then insert itself at random in locations in the genome that are expressed in the developing embryo or primitive uterus at the proper time, then promote fusion of membranes to permit the formation of a placenta, with all this happening at least six separate times in the six lineages tested so far? We should also make clear, expressing a syncytin by itself is unlikely to be enough to make a placenta, which is a complex organ requiring interactions between mother and embryo, and the ability to exchange nutrients and oxygen."

Pure argument from personal incredulity.

"Let me close by posing Torley’s questions to him, concerning syncytins:"

"Do you accept that if hypothesis A readily explains an empirical fact F and hypothesis B does not, then F (taken by itself) constitutes scientific evidence for A over B? Or putting it another way, if a fact F is predicted by hypothesis A, and compatible with hypothesis B but not predicted by B, then do you agree that F constitutes scientific evidence for A over B? If not, why not?"

Anne, you have no hypothesis. No mechanism. No explanation as to why the unidentifiable flying intelligent designer would place different syncytins, in different ERVs, in different chromosomes, in different lineages, embedded in fake structures mimicking retroviral proviruses, for no apparent purpose, all to do the same job. It just makes no sense.

"Evidence for and against common descent. It’s not nearly so open and shut a case as some believe, unless there is an a priori commitment to materialistic explanations."

It is a shut case for you because you won't open it, Anne. Time and again, we see cdesign proponentsist's arguments against the proof of evolution from ERVs, proof that is beyond any reasonable doubt, being ignored, and replaced by these desperate attempts at firefighting. Pure ignorance. I summarise that proof here. https://barryhisblog.blogspot.com/p/why-do-virologists-and-geneticists.html

Postscript.

Here is Anne Gauger representing the "Biologic Institute" by being filmed in front of a green screen upon which a shutterstock image of a real lab is used to promote the lie that intelligent designer spotting is science.

This from Wikipedia.

The Biologic Institute was a section of the Discovery Institute created to give the organization a facade of conducting biological research with the aim of producing experimental evidence of intelligent design creationism, funded by the Discovery Institute. It claimed offices in Redmond, Washington and laboratories in the Fremont neighborhood of Seattle, Washington. Instead Biologic Institute consisted solely of a rented office space in Redmond which is no longer in use for several years (since at least 2015) although the web domain is still renewed.

Gauger once contacted me via Facebook messaging to ask me about ERVs. I wish I had preserved a record of our exchange. She wanted to know why people think that ERVs are such slam-dunk evidence for evolution. It was a polite exchange in which I helped her, until she asked me for some relevant peer-reviewed scientific literature. So I sent her the contents of the reference section here, @ https://docs.google.com/document/d/17KaYjZ9zM7e8zkG2y9udqVG-NQJx-QP_Gjz1xzyt5Fk/edit?usp=sharing
Her response? She blocked me!

And now, just for fun, see https://web.archive.org/web/20120415012136/http://intelligentdesignr.org.uk/ ;)