Remember the “developmental hourglass”? Well, not so fast.

_{Denyse O'Leary

February 17, 2018

Darwinism, Evolution, Intelligent Design}

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“The hourglass model of embryonic evolution predicts an hourglass-like divergence during animal embryogenesis – with embryos being more divergent at the earliest and latest stages but conserved during a mid-embryonic (phylotypic) period that serves as a source of the basic body plan for animals within a phylum.”

Well, not so fast: From Hajk-Georg Drost, Philipp Janitza, Ivo Grosse, and Marcel Quint at Current Opinion in Genetics & Development:

• Developmental hourglass patterns are not specific for animals.

• In plants, developmental hourglass patterns are associated with embryogenesis and post-embryonic phase transitions.

• Morphological and transcriptomic patterns can be uncoupled.

• The organizational checkpoint hypothesis proposes that developmental reprogramming inevitably results in evolutionarily conserved transition periods.

The developmental hourglass model has its foundations in classic anatomical studies by von Baer and Haeckel. In this context, even the conservation of animal body plans has been explained by evolutionary constraints acting on mid-embryogenic development. Recent studies have shown that developmental hourglass patterns also exist on the transcriptomic level, mirroring the corresponding morphological patterns. The identification of similar patterns in embryonic, post-embryonic, and life cycle spanning transcriptomes in plant and fungus development, however, contradict the notion of a direct coupling between morphological and molecular patterns. To explain the existence of hourglass patterns across kingdoms and developmental processes, we propose the organizational checkpoint model that integrates the developmental hourglass model into a framework of transcriptome switches.
(public access) More.

“Organizational checkpoints” as a substitute? Sure, but that is design, not Darwin.

See also: Book review in New Scientist discusses the long-drawn-out “lies” of Ernst Haeckel’s fake embryos

and

Haeckel’s Embryos Are Alive (and now taking your calls in Darwinworld)

Comments

When building multithreaded software, you need to build checkpoints where the asynchronous threads synchronize/rendezvous, and stage their results for another set of threads to continue the process; where the threads' variable sets would become interdependent or the thread resources would be shared in an inviable fashion; otherwise you produce critical race conditions. I praise you because I am fearfully and wonderfully coded.LocalMinimum_{February 18, 2018
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The erroneous Darwinian presupposition that similar looking species are basically the same on the molecular level, as well as basically the same physiologically, is far from a harmless belief.,,,
What scientific idea is ready for retirement? – Mouse Models Excerpt: A recent scientific paper showed that all 150 drugs tested at the cost of billions of dollars in human trials of sepsis failed because the drugs had been developed using mice. Unfortunately, what looks like sepsis in mice turned out to be very different than what sepsis is in humans. Coverage of this study by Gina Kolata in the New York Times incited a heated response from within the biomedical research community. AZRA RAZA – Professor of medicine and director of the MDS Centre, Columbia University, New York http://www.theguardian.com/science/2014/jan/12/what-scientific-idea-is-ready-for-retirement-edge-org
a few more notes:
Animal Testing Is Bad Science: Point/Counterpoint Excerpt: The only reason people are under the misconception that animal experiments help humans is because the media, experimenters, universities and lobbying groups exaggerate the potential of animal experiments to lead to new cures and the role they have played in past medical advances.,,, The Food and Drug Administration (FDA) has noted that 92 percent of all drugs that are shown to be safe and effective in animal tests fail in human trials because they don’t work or are dangerous.,,, Physiological reactions to drugs vary enormously from species to species. Penicillin kills guinea pigs but is inactive in rabbits; aspirin kills cats and causes birth defects in rats, mice, guinea pigs, dogs, and monkeys; and morphine, a depressant in humans, stimulates goats, cats, and horses. http://www.peta.org/issues/animals-used-for-experimentation/animal-testing-bad-science.aspx Comparing the human and chimpanzee genomes: Searching for needles in a haystack – Ajit Varki1 and Tasha K. Altheide – 2005 Excerpt: we have many characteristics that are uniquely human. Table 1 lists some of the definite and possible phenotypic traits that appear to differentiate us from chimpanzees and other “great apes”2. For the most part, we do not know which genetic features interact with the environment to generate these differences between the “phenomes”3 of our two species. The chimpanzee has also long been seen as a model for human diseases because of its close evolutionary relationship. This is indeed the case for a few disorders. Nevertheless, it is a striking paradox that chimpanzees are in fact not good models for many major human diseases/conditions (see Table 2) (Varki 2000; Olson and Varki 2003). http://genome.cshlp.org/content/15/12/1746.full Mouse gene expression reveals “widespread differences” from humans - Nov. 22, 2014 Excerpt: an international group of researchers has found powerful clues to why certain processes and systems in the mouse — such as the immune system, metabolism and stress response — are so different from those in people.,,, Mice are widely used to model human metabolism, disease, and drug response. But results published today (November 17) in PNAS reveal widespread differences between human and mouse gene expression, both in protein-coding and noncoding genes, suggesting that understanding these disparities could help explain fundamental differences in the two species’ physiology. Michael Snyder of Stanford University and his colleagues compared how genes are expressed in 15 different human and mouse tissues, including brain, heart, liver, and kidney. They found that gene expression patterns clustered by species rather than tissues. For example, gene expression in a mouse liver more closely resembled the patterns observed in a mouse heart than those observed in a human liver. https://uncommondescent.com/genetics/mouse-gene-expression-reveals-widespread-differences-from-humans/ Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F Frequent Alternative Splicing of Human Genes – 1999 Excerpt: Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310997/ Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing - 2016 In Brief Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,, Page 806 excerpt: As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms (Smith and Kelleher, 2013). http://iakouchevalab.ucsd.edu/publications/Yang_Cell_OMIM_2016.pdf
bornagain77_{February 17, 2018
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When I attended UCLA, the refrain we heard over and over again in our Vertebrate Morphology class was "Ontogeny recapitulates phylogeny." While I found the class exciting, though being taught by someone passing through some kind of personal crisis, this was a statement more of dogmatism than actual fact. It was a given that seemed in no need of demonstration. In those days, I didn't give it much thought. Times, however, have changed. Taking a very quick look at this paper, they're saying that that the transcriptome--that is, what is being transcribed at any given instance of development, which varies with time--likewise goes through an "hourglass," or constraint. They say this might be accounted by, as well as the other types of 'hourglasses', including the morphological, by proposing what they call an "organizational checkpoint model." My intuition suggests that each developing organism must take stock of what's happening genetically, hence the 'checkpoint,' before continuing on to later development. The 'hourglass' here could easily be accounte for if we think of a transition beginning wherein some transcription is shut down before starting up the transcriptome of later development: i.e., Phase I of development shuts down, testing occurs that "all systems are go," and then the organism 'shifts' into a new developmental program, Phase II. "Organizational checkpoint": who designed that?PaV_{February 17, 2018
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and yet, although his work was (re)discovered to be fraudulent in 1997, they still referenced Haeckel's work in the paper, and the fakes still keep making cameos in textbooks.
Haeckel's Embryo Drawings Make Cameos in Proposed Texas Instructional Materials - Casey Luskin - June 2011 http://www.evolutionnews.org/2011/06/haeckels_embryos_make_multiple047321.html
PZ Myers even named his blog Pharyngula, and refuses to accept any evidence that contradicts his belief,,,
PZ Myers - blog https://freethoughtblogs.com/pharyngula/ Pharyngula Excerpt: The existence of a common pharyngula stage for vertebrates was first proposed by German biologist Ernst Haeckel (1834–1919) in 1874.[4] https://en.wikipedia.org/wiki/Pharyngula
and again, despite the refusal of some mainstream Darwinists to accept the truth, Haeckel's work is now known to be, besides fraudulent, just plain wrong:
Challenging the Precious Pharyngula - Casey Luskin - July 2011 http://www.evolutionnews.org/2011/07/challenging_the_precious_phary048291.html Three Flawed Evolutionary Models of Embryological Development and One Correct One - Casey Luskin - 2011 Excerpt: When biologists carefully compare embryological data, they find that there is considerable variability at the purported phylotypic stage, leading increasing numbers of biologists to question whether this pharyngular stage exists. As a paper in Nature said last year: "both the model and the concept of the phylotypic period remain controversial subjects in the literature." PZ generally refuses to address this literature, but it nonetheless calls into question the very concept that defines this model and gives PZ's Pharyngula blog its name. http://www.evolutionnews.org/2011/07/three_flawed_evolutionary_mode048541.html Vertebrate Gene Expression and Other Properties Don't Support a "Phylotypic" Stage - Casey Luskin - June 14, 2013 Excerpt: a new article in PLoS Genetics, "The Hourglass and the Early Conservation Models -- Co-Existing Patterns of Developmental Constraints in Vertebrates," shows that,, an analysis of the genome based on Darwinian assumptions fails to confirm many predictions of the "phylotypic" stage. ,,, (as they report),,, "During development, vertebrate embryos pass through a "phylotypic" stage, during which their morphology is most similar between different species. This gave rise to the hourglass model, which predicts the highest developmental constraints during mid-embryogenesis. In the last decade, a large effort has been made to uncover the relation between developmental constraints and the evolution of the genome. Several studies reported gene characteristics that change according to the hourglass model, e.g. sequence conservation, age, or expression. Here, we first show that some of the previous conclusions do not hold out under detailed analysis of the data." (Barbara Piasecka, Pawe? Lichocki, Sebastien Moretti, Sven Bergmann, Marc Robinson-Rechavi, "The Hourglass and the Early Conservation Models -- Co-Existing Patterns of Developmental Constraints in Vertebrates Barbara Piasecka," PLoS Genetics, Vol. 9(4) (April, 2013).),,, http://www.evolutionnews.org/2013/06/vertebrate_gene073171.html Threatening the Pharyngula--The Debate With PZ Myers on Evidence from Embryology - audio podcast - August 2011 http://intelligentdesign.podomatic.com/player/web/2011-08-03T16_46_23-07_00 The mouse is not enough - February 2011 Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.” http://www.the-scientist.com/news/display/57986/
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“Small problem, one of the most blatant examples of a known falsehood being taught as proof of evolution are Haeckel’s Embryo drawings.“ According to Wiki, Haeckel’s ‘ontogeny recapitulates phylogeny’ was discredited early in the last century. This certainly is consistent from what I remember from my introductory zoology classes in the mid 70s.
Since embryos also evolve in different ways, the shortcomings of the theory had been recognized by the early 20th century, and it had been relegated to "biological mythology"[1] by the mid-20th century.
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They mentioned Haeckel as a reliable authority on mid-embryogenic development? Small problem, one of the most blatant examples of a known falsehood being taught as proof of evolution are Haeckel's Embryo drawings. Though the drawings have been known to be fraudulent for over 100 years;
Ernst Haeckel - Evangelist for evolution and apostle of deceit Excerpt: In his book,, published in German in 1868,, Haeckel used the drawing of a 25-day-old dog embryo which had been published by T.L.W. Bischoff in 1845, and that of a 4-week-old human embryo published by A. Ecker in 1851–59.14 Wilhelm His, Sr (1831–1904), a famous comparative embryologist of the day and professor of anatomy at the University of Leipzig, uncovered the fraud. Prof. Wilhelm His showed in 1874 that Haeckel had added 3.5 mm to the head of Bischoff’s dog embryo, taken 2 mm off the head of Ecker’s human embryo, doubled the length of the human posterior, and substantially altered the details of the human eye. He sarcastically pointed out that Haeckel taught in Jena, home of the then finest optical equipment available, and so had no excuse for inaccuracy. He concluded that anyone who engaged in such blatant fraud had forfeited all respect and that Haeckel had eliminated himself from the ranks of scientific research workers of any stature.15,16,,, Despite this totally dishonest and grievously mischievous basis for the theory of embryonic recapitulation, and the fact that it has long since been discredited scientifically, the completely false idea that human beings retrace their evolutionary past in the womb has been taught as evidence for evolution in schools and universities in the past, and it is still included in many popular science books (to this day).18,19 http://creation.com/ernst-haeckel-evangelist-for-evolution-and-apostle-of-deceit Darwin Lobbyists Defend Using Fraudulent Embryo Drawings in the Classroom - Casey Luskin - October 11, 2012 Excerpt: embryologist Michael Richardson, who called them "one of the most famous fakes in biology," or Stephen Jay Gould who said "Haeckel had exaggerated the similarities by idealizations and omissions," and that "in a procedure that can only be called fraudulent," Haeckel "simply copied the same figure over and over again." Likewise, in a 1997 article titled "Haeckel's Embryos: Fraud Rediscovered," the journal Science recognized that "[g]enerations of biology students may have been misled by a famous set of drawings of embryos published 123 years ago by the German biologist Ernst Haeckel." ,,, So if you're a Darwin lobbyist defending a textbook that uses Haeckel's inaccurate drawings, be forewarned: neither Bob Richards nor any other credible authorities I'm aware of endorse the unqualified and uncritical use of Haeckel's original inaccurate drawings in biology textbooks today. You're on your own. - per Evolution news Haeckel's Bogus Embryo Drawings - video http://www.youtube.com/watch?v=ecH5SKxL9wk Icons of Evolution 10th Anniversary: Haeckel's (Bogus) Embryos - January 2011 - video http://www.youtube.com/watch?v=lAC807DAXzY There is no highly conserved embryonic stage in the vertebrates: - Richardson MK - 1997 Excerpt: Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel's drawings, http://www.ncbi.nlm.nih.gov/pubmed/9278154 Side by side comparison of Haeckel's drawings to actual photographs http://www.ichthus.info/Evolution/PICS/Haeckel-2.jpg Other embryo photographs by Richardson that make the point that they are VERY DIFFERENT: http://www.ichthus.info/Evolution/PICS/embryo3.jpg
This is all interesting because Charles Darwin himself considered this fraudulent embryo evidence from Haeckel as the 'strongest class of facts' in favor of his theory:
"The embryos of the most distinct species belonging to the same class are closely similar, but become, when fully developed, widely dissimilar." This is,,, "by far the strongest single class of facts in favor of my theory." Charles Darwin - Origin of Species (1859), Letter to Asa Gray (1860) The Strongest Single Class of Facts – 2011 Excerpt: “Embryology is to me is by far the strongest single class of facts in favor” of my theory of evolution, was the claim of Charles Darwin. The nineteenth century embryological evidence was pivotal for the development of Darwin’s theory of evolution. Just two months before the release of the first edition of The Origin of Species in September 1859, Darwin wrote to Charles Lyell, “Embryology in Chapter VIII is one of my strongest points I think.” http://www.darwinthenandnow.com/2011/11/the-strongest-single-class-of-facts/
Thus if the best evidence for Darwinian evolution is found to be fraudulent, Darwinian excuse making aside, what does this say about the rest of the theory? as to this comment from the article:
"contradict the notion of a direct coupling between morphological and molecular patterns."
The disconnect between molecules and morphology is far greater than they apparently realize. For example:
Heads or Tales by Casey Luskin - Fall 2014 Excerpt: They concluded that the evidence is "contrary to the evolutionary hourglass model," and that it shows "considerable variability—and evolutionary lability—of the tailbud stage, the purported phylotypic stage of vertebrates." In their view, this "wide variation in morphology among vertebrate embryos is difficult to reconcile with the idea of a phylogenetically-conserved tailbud stage."3 These patterns hold true not just for physical characteristics of development, but also for important properties of the genome. A 2013 article in PLoS Genetics found that genomic properties related to DNA sequence, gene age, gene family size, and gene expression did not match the convergent patterns predicted by the phylotypic stage. http://www.salvomag.com/new/articles/salvo30/heads-or-tails.php "The earliest events leading from the first division of the egg cell to the blastula stage in amphibians, reptiles and mammals are illustrated in figure 5.4. Even to the untrained zoologist it is obvious that neither the blastula itself, nor the sequence of events that lead to its formation, is identical in any of the vertebrate classes shown. The differences become even more striking in the next major phase of in embryo formation - gastrulation. This involves a complex sequence of cell movements whereby the cells of the blastula rearrange themselves, eventually resulting in the transformation of the blastula into the intricate folded form of the early embryo, or gastrula, which consists of three basic germ cell layers: the ectoderm, which gives rise to the skin and the nervous system; the mesoderm, which gives rise to muscle and skeletal tissues; and the endoderm, which gives rise to the lining of the alimentary tract as well as to the liver and pancreas.,,, In some ways the egg cell, blastula, and gastrula stages in the different vertebrate classes are so dissimilar that, where it not for the close resemblance in the basic body plan of all adult vertebrates, it seems unlikely that they would have been classed as belonging to the same phylum. There is no question that, because of the great dissimilarity of the early stages of embryogenesis in the different vertebrate classes, organs and structures considered homologous in adult vertebrates cannot be traced back to homologous cells or regions in the earliest stages of embryogenesis. In other words, homologous structures are arrived at by different routes." Michael Denton - Evolution: A Theory in Crisis - pg 145-146 Darwinism vs Biological Form https://www.youtube.com/watch?v=JyNzNPgjM4w
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