Universal common ancestry in the hot seat V

Vincent Torley Thinks I Have Egg on My Face
Ann Gauger 

Well, I must say I didn't expect to be honored by a 7500-word broadside by philosopher Dr. Vincent Torley, assisted by Dr. Josh Swamidass, Assistant Professor at Washington University. I guess they must have a lot of spare time. The reason for the post at Uncommon Descent? Both hold common descent to be absolutely, incontrovertibly, obviously true, and they apparently wish I would fall into line and stop embarrassing them by doubting common descent. They wish I would give up my "peculiar kind of intellectual obstinacy."

The argument is in the end all about common descent. (There are a few accusations of poor reasoning, obscuring the issue, and even a little bad faith along the way.) Look, intelligent design is not wedded to common descent. Neither is it wedded to a denial of common descent. Intelligent design states that there is evidence of design in the universe. I think we are in agreement on this point. In terms of biology, how the designer instantiated that design is still subject to debate, based on the strength of the evidence for each position.

As a biologist, I see evidence on both sides of the debate. The evidence is equivocal -- hence the fact that ID advocates take different positions on the subject. Yet common descent -- the idea that organisms descend from one or a few common ancestors -- is treated like a sacred cow by many scientists, and even, it appears, by some philosophers. Indignation arises that anyone would doubt it, would even have questions. Scientists take common descent as axiomatic, and accept evidence that is itself interpreted through a lens of common descent as proof of common descent. As a consequence, any evidence against common descent meets opposition and is explained away.

So when I see weak evidence for common descent I say so, as I did in a post here, "The Vitellogenin Pseudogene Story: Unequally Yolked." (Apparently Dr. Torley caught the reference but missed the yolk, as he repeatedly misstates my post's subtitle as "Unequally Yoked.") I wrote the aforementioned post because of weak evidence, and even an overstatement of the evidence by some.

The controversy began with the post on vitellogenin synteny, "Vitellogenin and Common Ancestry: Reading Tomkins," by Professor Dennis Venema at Trinity Western University, where I read some interesting arguments regarding cross-species synteny in the region of the chicken vitellogenin genes. Synteny is the term for the shared arrangement of genes along chromosomes from different organisms, and its existence is taken as evidence for common descent. Vitellogenins are egg yolk proteins, present and used in egg-laying organisms.

I followed up by reading the paper "Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation," by David Brawand, Walter Wahli, and Henrik Kaessmann, on which Venema's post was based. (It's free access. You can verify all this yourself.) It's always a good idea to read the original material and evaluate the evidence for yourself. What I saw in Brawand et al. is what prompted me to write my post.

My dispute with Torley (and Venema) is at bottom a dispute about the scientific interpretation of data, or should be. Therefore I am going to go through the data in some detail, to show why I reached the conclusions I did with regard to the human "VIT1" pseudogene, and where we differ in interpretations. This essentially covers Torley's points 1 and 2. I will address the points 3-7 in later posts, so as not to burden the reader with excess length.


There are three chicken egg yolk genes, VIT1, VIT2, and VIT3, all expressed and made into protein because chickens lay eggs. The Brawand paper set out to see if there was any evidence for a vitellogenin presence in the human genome, with the idea that we are descended from an egg-laying animal. They looked in the region of our chromosome that is analogous to the chicken genome, and aligned the two against each other. A dotplot from the Brawand paper (see below) shows where the human (Y axis) and chicken (X axis) DNA sequences align. A perfect alignment (for example if human sequence was aligned against human) should show a diagonal solid line.




All figures taken from Brawand, D., Wali, W., and Kaessmann, H. 2008. Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation. PLoS Biology (6) 507-517. Creative Commons license.

The top panel illustrates the VIT1 alignment between the two sequences, chicken and human, and the bottom panel VIT2 and VIT3. Black dots show where sequence similarity exists. The colored stripes indicate coding sequences (exons) for each "gene." In between in the white regions are the non-coding introns and intergenic spaces (sequences between genes). ELDT1, FP, SSX2IP, and CTBS are functional genes in both human and chicken and show sequence similarity and synteny in all coding sequences (the yellow stripes). Even some intergenic spaces show evidence of synteny. Where the synteny disappears is where the VIT1, VIT2, and VIT3 coding sequences should be.


I found the VIT1, VIT2, and VIT3 alignments to be ambiguous at best. However, in the supplemental materials for the Brawand paper is another representation of the syntenic regions where the human VIT1, VIT2, and VIT3 remnants should be. That makes things clearer. It is reproduced below, but click on the image to see the figure properly:



The bars colored red and black represent the chicken VIT genes, showing only their exons (the parts of the gene that contribute to making protein), alternating as red and black segments along the VIT sequences. (There are 35 exons in VIT1 and 2, 36 exons in VIT3.) Above each bar and running parallel to it are thin red lines, indicating where similarity has been detected, with insertions, deletions and stop codons necessary to make the sequence line up also indicated. To find this alignment they used "highly sensitive similarity search algorithms," and ran repeated trials. From the paper:

The best scoring alignment chain was determined from the 2,000 best local alignments for each VIT region using dynamic programming. Importantly, the combined alignments of VIT coding sequences of the best chain for each of the opossum VIT1-VIT3 regions (aligned to chicken) showed significantly higher alignment scores than the genomic background (introns and intergenic regions) in the chain, as assessed by a Mann-Whitney U test (P < 0.05). This suggests that the obtained (pseudogenic) VIT remnants from opossum are nonrandom sequence matches and represent true VIT sequences. In the eutherian [human and dog] comparison, VIT1 coding sequences showed significantly higher scores than the genomic background [reported as P < 0.05 elsewhere] (the alignable regions for the other two VIT genes may be too short to provide statistical significance -- VIT3 -- or represent spurious matches -- VIT2). [Emphasis added.]
There was very little actual sequence alignment data given for the human syntenic regions, just the 150 base sequence from exon 3 that I mentioned in my post. Since I was asked to provide the source of my analysis, here is it, as obtained in the paper in a supplementary figure; again, click on the image to see it better:


Full disclosure: this is the best-reported evidence they have for human synteny. The rest is unconvincing to me, though it may be convincing to others. Surely if they had a better or more extensive alignment they would have reported it. This by the way, I would assume is the stretch of DNA used by Jeff Tomkins in his analysis of the region.

Now for a general comment regarding the accusation of faulty statistics made against me by Torley and Swamidass. Here is the segment from Torley's post:

Professor Swamidass has two comments which are germane here. First, he points out that as a matter of standard practice, the data relating to similarity in the paper by Brawand et al. should be considered correct, unless proven otherwise. If Dr. Gauger thinks that the authors' claims of similarity are doubtful, then I would invite her to show the exact DNA sequence she used, so that interested readers can perform a BLAST by themselves (there is a website for this), to verify both the match to the vitellogenin chicken gene and to the human sequence. This doesn't resolve the issue of picking the right DNA sequence, but it is a start. Selecting the right parameters is important, too: if you use the wrong gapped parameter (a mistake Tomkins is notorious for making), then there will be discrepancies. [Emphasis added.]
I do not question the authors' data, but I do question their interpretation that it proves there is a VIT1 pseudogene in humans. Actually to be fair, they merely suggest it as evidence. They do not go much further than what I have quoted above: they point out a few deletions held in common by dogs, humans, and armadillo in the 150 base sequence I show above, arguing that they all share common ancestry. The bulk of the paper is about the remnants of opossum and platypus vitellogenin genes, perhaps because they recognize that the evidence is weak for dogs (for which they report no analysis I could find) and humans.

About the data being correct and my questioning it: All scientists are (or should be) taught in graduate school to critically evaluate conclusions. That is not the same as questioning original data, which I do not do. Questioning conclusions, evaluating them carefully to see if they are warranted, is something all scientists should do.

Again, I based my analysis on the data reported in the paper; I did not question the underlying data. The 150 base sequence I talked about was available as a supplementary figure in the paper itself, and I have already shown it to you. Careful reading of Brawand et al. would have revealed it -- it is the only sequence reported for human alignments. But since I am asked to provide the sequence I used, here it is. The 50 percent identity that is so disputed was simply calculated based on the percent identical positions for this 150 base alignment. I used the authors' own data. By the way, nowhere do they report a sequence identity for the region, probably because with poor alignment elsewhere, the percent identity would be considerably lower than 50 percent.

Lastly, I don't know where Torley's computer scientist friend Glenn Williamson got his figures, but they do not match the data reported in the paper. Says Williamson:

About 1,500 base pairs can be aligned with around 73% identity. That's much more than the 150 base pairs that Tomkins chose to focus on. Readers will recall that Tomkins claimed only a 62% identity, even for this short segment. [Emphasis in the original.]
If the alignment was as high as Williamson said over such a long stretch, surely it would have been reported by the authors. It certainly doesn't agree with the figures I have shown from the original paper itself. (See Figure S1 and S2.) The 150 base alignment shown in figure S2, with its 50 percent identity, is the little segment on the left side of VIT1, directly over exon 3 in Figure S1. There is no other alignment around it, let alone 1500 bases with 73 percent identity. I'll leave readers to judge whether Williamson's alignments are valid. But as Torley says, "if you use the wrong gapped parameter then there will be discrepancies."

Now for why I wrote the post. For this you will have to go to Dr. Dennis Venema's post that started it all, and which was mentioned earlier. (I do not think it is under the Creative Commons license so I won't reproduce his figure here.) I want you to compare his "redrawings" of the synteny between humans and chickens in the VIT1, VIT2, and VIT3 genes to the actual data reported in Brawand et al.'s paper. Does Venema's redrawing strike you as an exaggeration of the synteny for VIT1, as it did me? Compare it to the figures I have shown here from the original paper.

If all people did was to read Venema's post, the synteny would look pretty convincing. That's unfortunate. Those not trained in science will take his post at face value, and be convinced of VIT1 synteny and its status as a former vitellogenin gene. When the original data is examined, it's not nearly as convincing. Scientists have a duty to represent data accurately, even other people's data. Now I may not have access to information Dennis Venema has, so I will give him the benefit of the doubt. But I would be happier if he changed his figures, or revealed his source for any data that didn't come from the paper he cited.

Finally, Torley makes a point about my having commented that the opossum alignment might show synteny better than the human or dog sequence. I didn't discuss it in my post beyond that comment because it wasn't the focus of my argument. I will turn to the discussion of the alignment between opossum and other genomes with the chicken, and the evidence for pseudogenes in another post. I will also answer Torley's question about logical inferences, and offer him my own logical puzzle.

I will deal with his other accusations along the way.

Thanks for sticking with the nitty-gritty analysis, dear readers. It's up to you to decide what you think about human synteny with VIT genes, whether it is strongly or weakly supported by the evidence, and whether we are justified in considering alternate explanations.

Information and the design debate

Too much of a good thing?

Objection to Intelligent Design -- Universe Is Too Big, with Too Much "Wasted Space"

David Klinghoffer

Thoughtful reader Eric points me to a fine article over that The Stream by Tom Gilson, addressing an objection to ID:

We don't know whether anyone is enjoying the view from some other planet. For all we know, we might be the only observers. Whether we are or not, the vastness of it all has led some skeptics to ask, why would God waste so much space on so few living creatures? Is this really a mark of intelligent design? It might surprise you to hear that I like that question, but I do: I enjoy answering it.

One of the better-articulated versions of that question goes like this:

Doesn't the way that 99.99999999% of the universe is absolutely inhospitable to any kind of life show you that it wasn't made for anybody? It is easy to imagine how a universe could have been more intelligently designed, with less wasted space and energy and more hospitality for life.

This objection is formulated by John R. Shook, of the Center for Inquiry, who also teaches philosophy at the University of Buffalo ("The Disappearing God"). Gilson goes on:

First, the "scientific" viewpoint of all this emptiness, when taken in full perspective, makes no strong statement against design. Quite the contrary, actually. I could mention the universe's fine-tuning for life, for one thing. For another, we know now that a large universe is necessary for life, at least according to physics as we understand it.

On that, Gilson cites "the principle of the galactic habitable zone."

[Its] implications include the principle that a certain amount of empty space, but not too much, is essential for life to thrive. (That's admittedly an oversimplification which I make for the sake of space here on the blog, but not, I take it, a distortion.) So it is premature at best to suppose that large amounts of space "inhospitable to any kind of life" really mean that "it wasn't made for anybody."

Second, that idea is not just premature; it's also incredibly short-sighted with respect to who Christians understand God to be. Is God concerned about the waste of energy and space?

Eric adds:

I think there is at least one other point that could be made. How does one recognize when something is rare? We see the extremely unusual state of this privileged planet precisely because it is in stark contrast to a vast inhospitable universe.

And we can see that contrast because we are also unusually suited for observation and scientific discoveries. Our state is both fine-tuned and knowable as fine-tuned.

Contrary to what Dr. Shook imagines, a vast universe is a key component in at least one line of argument for intelligent design. Articulated by Michael Denton and others, this argument points to the unique fitness of the universe and of our planet for upright bipeds like ourselves. The whole thing appears set up for us, and only for us. The vaster the cosmos, the more dramatically that point is underlined.

Denton's current focus is on the fitness of the universe for fire-using creatures like us. See the short documentary Fire-Maker.

What exactly is the size of the universe, as we observe it? Wikipedia says:

The proper distance -- the distance as would be measured at a specific time, including the present -- between Earth and the edge of the observable universe is 46 billion light-years (14 billion parsecs), making the diameter of the observable universe about 91 billion light-years (28×109 pc).

As Evolution News observed yesterday in a biological context, ID critics often end up playing the role of naïve theologian: What they "seem to want is a metric with The Human Body as God Would (or Should) Have Made It at one end of the measuring stick. As Dilley and Nelson have pointed out, contemporary Darwinian evolutionary thinking borrows heavily from theology for its justification." In this case it should be The Universe as God Would (or Should) Have Made It.

I'd want to ask John Shook, is it like going to the mall and looking for a pair of pants with the right waist and inseam measurements? 91 billion light-years is too big to be intelligently designed. Is there a size that would be too small? Just right?

Merely to ask such questions is to see how absurd the contention is that the universe has too much "wasted space."

Darwinism vs. the real world XXXIII

Liver Function and Its Effects
Howard Glicksman 

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News is delighted to offer this series, "The Designed Body." For the complete series, see here. Dr. Glicksman practices palliative medicine for a hospice organization.

Tim (not his real name) was a hard-working, hard-drinking man who had never stayed attached to anyone. He had contracted viral hepatitis which, combined with his alcohol abuse, had caused him to develop chronic liver disease. He had been hospitalized several times when I first met him at his sister's home after he was placed in hospice care. He was lying in a recliner looking pretty weak with a yellowish tinge to the whites of his eyes and skin. He had marked muscle wasting, scattered scratches and bruises on his arms, and a large belly with swollen red legs. I saw that he was confused and had problems expressing himself, so I turned to his sister and her son to get the history.

They told me that Tim had been declining for the last several weeks and that, although he had stopped drinking a few months ago, each time he came out of hospital he was worse than the last time. Now he needed a lot of help to dress, bathe, and use the bathroom. He could barely stand, even with significant assistance, to pivot and transfer to a wheelchair. He was more prone to confusion and slept most of the time, seemed to be itchy, ate very little and complained of abdominal and leg swelling and pain. When I examined him, not only was he confused and jaundiced, I also found that he had a fever, a quick pulse, and a relatively low blood pressure. I also noted that not only was his abdomen full of fluid but the redness in his swollen legs was due to infection.

His sister brought out the results of some of his recent blood work, which showed a very low serum albumin, elevated bilirubin and ammonia levels, and a moderate delay in his clotting test. I sat down with Tim's sister and nephew to explain the situation and what we might be able to do for him to keep him comfortable.

Next to the brain, the liver is the most versatile organ, performing over five hundred different tasks, and each is important for survival. Since the liver is capable of regeneration and has a large functional reserve, it usually requires a loss of over eighty percent of its cell function for the symptoms and signs of chronic liver disease to manifest. It is the liver that handles the metabolism of carbohydrates, proteins, and fats for the energy and nutrient needs of the body. It produces numerous different proteins for specific tasks and, using enzymes, chemically breaks down drugs, hormones and other substances so the body can maintain control of its chemical environment.

Evolutionary biologists are good at imagining how an ultra-complex organ like the liver could have come into being by talking about how it looks, but not how it actually works within the laws of nature to keep the body alive. But real numbers have real consequences and by using Tim's case to highlight just five of the over five hundred functions of the liver, we will see what would have happened to our earliest ancestors without any one of them. After all, evolutionary biology claims that life came about by chance and laws of nature alone, so it must explain how transitional organisms survived as the liver gradually acquired these vital functions while macroevolution was taking place.

First, the liver helps the body break down red blood cells and, using enzymes, chemically converts hemoglobin into bilirubin. It then takes bilirubin and joins it with cholesterol and other chemicals it produces to form bile. The liver sends the bile into the intestine so it can absorb fats and with it fat-soluble chemicals like vitamin A, for vision, vitamin D, for bones and calcium metabolism, and vitamin K, for clotting, all of which were necessary for our earliest ancestors. Just as we see for Tim, when the liver cells aren't working properly, the bilirubin they produce backs up and moves into the blood, making the bilirubin level rise and causing the whites of the eyes and the skin to turn yellow (jaundiced). People who are jaundiced often feel tired and weak, with a poor appetite and nausea, and may feel itchy.

Second, the liver produces albumin which represents over sixty percent of its entire protein output. One role for albumin is to help transport minerals like calcium and magnesium, fatty acids and other lipids, and steroid hormones like estrogen, progesterone, and testosterone in the blood so they can travel to where they are needed in the body. But one other very important function of albumin is to maintain the blood volume by keeping enough water in circulation. As blood enters the arterial side of the capillary under pressure and moves to the venous side, water is naturally pushed out of the circulation through the pores within the walls of the capillary and into the interstitial fluid, like soft boiled potatoes through a ricer.

Since albumin cannot escape from circulation through the walls of the capillary, it naturally applies an osmotic pull back on the water trying to leave, acting as a counterbalance to the pressure pushing the water out. The degree of osmotic power applied by albumin to pull back on the water trying to escape from circulation is directly related to how much albumin is in the blood. When the liver doesn't produce enough albumin, more water tends to move out of the circulation and into the interstitial fluid, which reduces the blood volume and can cause blood pressure to drop. One of the main causes of Tim's low blood pressure and increased fluid in his abdomen (ascites) and legs (edema) was due to a very low level of albumin in his blood.

Third, besides albumin and other transport proteins, the liver produces most of the clotting factors. Hemostasis is the process by which the body prevents itself from bleeding, something that would have been vital for the survival of our earliest ancestors. Damage to the blood vessel wall triggers the muscles surrounding it to contract and close off the opening as much as possible. It also causes the platelets in the blood passing by to stick together, forming a soft plug to cover the opening and limit blood loss.

But, for many blood vessel injuries, this is not adequate to achieve hemostasis. The clotting factors must swing into action to produce a fibrin clot strong enough to permanently seal the defect, stop the bleeding, and allow healing to take place. When the clotting factors are released from the liver into the blood they are inactive and do not interact with each other unless they encounter a damaged blood vessel. This is very important because if fibrin clots formed within normal blood vessels they could block blood flow and lead to organ damage and death. When the clotting factors encounter a damaged blood vessel, and the platelet plug trying to seal it, this triggers them to interact like dominos to form a fibrin clot in a process called the coagulation cascade. When the liver isn't making enough clotting factors, this makes the body prone to bleed easier as we see with Tim, whose clotting test was prolonged. That was why his arms were bruised due to minimal trauma from scratching.

Fourth, another set of proteins the liver makes is complement which consists of over thirty proteins that, when activated, work together to help the immune cells fight infection. Just like the clotting factors, the complement proteins are inactive when the liver releases them into the blood. Encountering microbial infection triggers them to interact like dominos to aid in the immune defense of the body. They increase inflammation in the area of infection, kill microbes, and attract immune cells to the battlefield and help them attach to microbes so they can literally swallow and destroy them. When the liver isn't working as well as it should, it produces less complement, which along with other factors, makes the body more susceptible to infection. Clinical experience shows that this would have made the survival of our earliest ancestors impossible.

Fifth, another important job for the liver is to convert ammonia, a highly toxic byproduct of protein metabolism, into urea, so it can be released from the body through the kidneys.

This requires five specific enzymes working together in what is called the urea cycle. Elevated blood levels of ammonia are toxic to the nervous system and the absence of any one of these five enzymes would have made life impossible for our earliest ancestors. When the liver isn't working properly, it may allow ammonia, and other toxic substances that it usually metabolizes, escape into the blood, causing a condition called hepatic encephalopathy. In its milder form, this manifests as irritability, poor attention, anxiety, and insomnia. But if the ammonia level rises further, this can progress to imbalance, lethargy, confusion, slurred speech, difficulty swallowing, and be fatal. Returning to Tim, we see that with his confusion, difficulty speaking, and need for lots of assistance, that he is probably showing signs of hepatic encephalopathy.

Having detailed to his sister and nephew what was going on with Tim, I also explained that his leg infection could be responsible for his functional decline and confusion. In other words, if we could treat some of his problems with medications and provide him with good nutrition and support, he may improve and be able to live a little longer. We started him on antibiotics to treat his infection, diuretics to push excess salt and water out of his body and reduce the swelling in his legs and abdomen, and medication to reduce the ammonia level in his blood. Over the next several weeks Tim's condition improved so that he was lucid, had a better appetite, and could be up on his own with a walker. The transformation was remarkable and he became very animated about how he had a "new lease on life."


Tim's nephew was due to go back to college for his pre-med courses in biology and he was perplexed. He believed in neo-Darwinism, and was exposed to the rhetoric that those who don't believe Darwin really don't understand science. But what he had learned about the liver and just five of its vital functions, and what he had seen happen over the last several weeks, gave him pause. He had seen someone who believes in intelligent design prove his knowledge of how science, and life, really works by bringing his uncle back from the brink. I told him that being a physician means having the responsibility to seek out and speak the truth so that those who are vulnerable will not be misled and being humble enough to admit that we don't always have all of the answers, and probably never will.

It was just a matter of time.

Oregon court allows resident to change sex from female to nonbinary
Faith Karimi and Dani Stewart, CNN

regon resident Jamie Shupe, who identifies as neither male nor female, can legally be considered nonbinary, a judge ruled.

In what legal experts believe is the state's first such ruling, Judge Amy Holmes Hehn ruled Friday that Shupe's sex has been changed from female to nonbinary.
READ: One transgender woman's long road to finding herself
"It feels amazing to be free from a binary sex classification system that inadequately addressed who I really am, a system in which I felt confined," the Portland resident said.

The Army veteran was assigned the gender of male at birth, but Shupe started transitioning to a female in 2013, more than a decade after leaving the military, according to The Oregonian newspaper.
Shupe said male or female titles didn't seem fitting, and preferred to use the first name, Jamie, instead of a pronoun. In April, Shupe filed a petition for a gender change.
"Oregon law has allowed for people to petition a court for a gender change for years, but the law doesn't specify that it has to be either male or female," said civil rights attorney Lake J. Perriguey, who filed the petition.

"The law just says, 'change.' Historically, people have asked for a gender change from male to female and the other way around, but Jamie is the first to ask for the gender of "nonbinary," Perriguey, said.
The lawyer said the standard form provided by the court clerk listed only male or female as options, so he inserted "nonbinary."
Their wish was granted Friday.
The judge said she has determined Shupe underwent surgical, hormonal or other treatment for the purpose of gender transition.

"The sexual reassignment has been completed," the judge wrote in the ruling. "No person has shown cause why the requested general judgment should not be granted."

All in the family? II

Inbred Neanderthals damaged us all

. From ScienceDaily:

The Neanderthal genome included harmful mutations that made the hominids around 40 percent less reproductively fit than modern humans, according to new estimates. Non-African humans inherited some of this genetic burden when they interbred with Neanderthals, though much of it has been lost over time. The results suggest that these harmful gene variants continue to reduce the fitness of some populations today. The study also has implications for management of endangered species.

Some time or other, these people should meet up with the Population Bomb crowd. Will they mutually self-destruct?

Incidentally:

Harris and Nielsen’s simulations also suggest that humans and Neanderthals mixed much more freely than originally thought. Today, Neanderthal sequences make up approximately 2% of the genome in people from non-African populations. But Harris and Nielsen estimate that at the time of interbreeding, closer to 10% of the human migrants’ genome would have been Neanderthal. Because there were around ten times more humans than Neanderthals, this number is consistent with the two groups acting as as single population that interbred at random. Recent DNA evidence has confirmed that the Neanderthal contribution to Eurasian genomes was higher in the past. Paper. (public access) – K. Harris, R. Nielsen. The Genetic Cost of Neanderthal Introgression. Genetics, 2016; DOI: 10.1534/genetics.116.186890 More.

So Neanderthals were not a “different species.”

See also: Neanderthal Man: The long-lost relative turns up again, this time with documents

Civil war.VII

Denis Noble: Evolution needs replacement, not extension

Posted by News under Darwinism, Epigenetics, Evolution, horizontal gene transfer

In The Paradigm Shifters: Overthrowing “the Hegemony of the Culture of Darwin,” Oxford’sDenis Noble explains to Suzan Mazur why our understanding of evolution needs to be replaced, not merely extended:

The reasons I think we’re talking about replacement rather than extension are several. The first is that the exclusion of any form of acquired characteristics being inherited was a central feature of the modern synthesis. IN other words, to exclude any form of inheritance that was non-Mendelian, that was Lamarckian-like, was an essential part of the modern synthesis. What we are now discovering is that there are mechanisms by which some acquired characteristics can be inherited, and inherited robustly. So it;s a bit odd to describe adding something like that to the synthesis (i.e., extending the synthesis). A more honest statement is that the synthesis needs to be replaced.

By “replacement” I don’t mean to say that the mechanism of random change followed by selection does not exist as a possible mechanism. But it becomes one mechanism amongst many others, and those mechanisms must interact. So my argument for saying this is a matter of replacement rather than extension is simply that it was a direct intention of those who formulated the modern synthesis to exclude the inheritance of acquired characteristics. (p. 27)

He goes on to say that the modern synthesis is a “gene-centric” view that has got causality in biology wrong.

Once Darwinism (random change followed by selection) is evaluated on the basis of probability, an entire metaphysic is going to collapse. That’s what Darwin’s followers have fought so hard to prevent.

Fear and loathing of design?

Medicine and Our "Perfect" Anatomy

Evolution News & Views 

Check out the title on this article from the current issue of the Journal of Experimental Zoology Part B: "Links Between Evolution, Development, Human Anatomy, Pathology, and Medicine, with a Proposition of a Re-defined Anatomical Position and Notes on Constraints and Morphological 'Imperfections,'" by Diogo and Molnar. The word in scare quotes, "imperfections," is your tipoff.

From the Abstract (emphasis added):

Surprisingly the oldest formal discipline in medicine (anatomy) has not yet felt the full impact of evolutionary developmental biology. In medical anatomy courses and textbooks, the human body is still too often described as though it is a "perfect machine." In fact, the study of human anatomy predates evolutionary theory; therefore, many of its conventions continue to be outdated, making it difficult to study, understand, and treat the human body, and to compare it with that of other, nonbipedal animals, including other primates. Moreover, such an erroneous view of our anatomy as "perfect" can be used to fuel nonevolutionary ideologies such as intelligent design.

Where to start? ID isn't an ideology, but a scientific reading of the agreed evidence of biology and other disciplines. It's not "non-evolutionary" -- at least they didn't say "anti-evolution" or "anti-science." Arguably, ID is atheory of evolution, inferring a cause behind life's long history of change, just not a Darwinian theory that insists on biology as the product of blind churning.

Beyond these familiar points, we don't know of any anatomy textbook -- certainly none we have ever seen or owned -- that describes human anatomy as "perfect."

Medical practice, physiology, anatomy, and other sciences of the human body do require, of course, concepts of normal structure and function, in order to have any sort of metric for assessing disease, etc. This isn't prima facie a question of ID or not, but simply what the logic of "healthy/diseased" necessitates.

What about the notion that medicine, being weighed down by a faulty view of our anatomy as "perfect," finds it "difficult" to "compare [the human body] with that of other, nonbipedal animals"? No, nursing students dissect cats, not humans, precisely because of their parallels (and less expense). Any medical student who went through AP and college biology likely had to dissect a fetal pig. Who says there are no comparisons made?

Design, anyway, is an inference to the best explanation for bodies. Whatever kind.

What Diogo and Molnar seem to want is a metric with The Human Body as God Would (or Should) Have Made It at one end of the measuring stick. As Dilley and Nelson have pointed out, contemporary Darwinian evolutionary thinking borrows heavily from theology for its justification -- a borrowing, incidentally, to which the theory is strictly not entitled, given the rule of methodological naturalism.

What our wannabe overlords are plannimg for the rest of us.

Treating religious beliefs as a form of mental illness

While we all sleep, our betters have plans for us.

From Digital Journal:

Kathleen Taylor, a neurologist at Oxford University, said that recent developments suggest that we will soon be able to treat religious fundamentalism and other forms of ideological beliefs potentially harmful to society as a form of mental illness.

She made the assertion during a talk at the Hay Literary Festival in Wales on Wednesday. She said that radicalizing ideologies may soon be viewed not as being of personal choice or free will but as a category of mental disorder. She said new developments in neuroscience could make it possible to consider extremists as people with mental illness rather than criminals.

She told The Times of London: “One of the surprises may be to see people with certain beliefs as people who can be treated. Someone who has for example become radicalized to a cult ideology — we might stop seeing that as a personal choice that they have chosen as a result of pure free will and may start treating it as some kind of mental disturbance.” More.

Has anyone noticed how these types speak as if their own axioms are a “surprise” or, elsewhere,“counterintuitive”?

Darwinism vs. the real world. XXXII

How the Body Controls Its Calcium

Howard Glicksman 

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News is delighted to offer this series, "The Designed Body." For the complete series, see here. Dr. Glicksman practices palliative medicine for a hospice organization.

When an archaeologist finds what she thinks may be a human artifact, she would ordinarily ask herself about its origin and function. The archaeologist knows that to identify such an artifact, the object must show evidence of having been produced by human intelligence, for a purpose. If she had found some rounded pieces of bronze that looked like they could be fit together to form a helmet, would she think that they had come about only by chance and the laws of nature? Of course not. She would know that bronze is a manmade alloy of copper and tin and that a helmet is used to protect the human skull and the brain within it from injury.

Evolutionary scientists, for their part, find skulls of different animals, which not only protect the brain from injury, but also have openings for the eyes, nose, and mouth. However, without considering what it takes to produce and maintain these structures, they claim that skulls arose unguided by purely natural processes, demonstrating the validity of Darwinian theory.
In the last few articles in this series, I have shown that the production and maintenance of the human skeleton requires multiple coordinated parts and process. It needs cells called osteoblasts and osteoclasts, the movement of calcium back and forth from the blood as the bone acts as a reservoir for the calcium needs of the body through its tissue fluid, and the presence of activated Vitamin D to bring in enough calcium from the gastrointestinal system. In addition, the body must have Ca++ ions in the blood for clotting. It needs calcium pumps in the cells to keep the Ca++ ion concentration of the cytosol ten thousand times less than the blood so it can signal proper nerve, gland, heart, and all other muscle function. When anyone looks at a skeleton, this is what they should know before they try to figure out where it came from.
But even that's not enough when taking into account how the bones relate to the body's calcium metabolism. For when it comes to life, real numbers have real consequences. Clinical experience teaches that not just any Ca++ ion concentration in the blood will do. It has to be the right amount. The normal blood level for calcium is between 8 to 10 units and if it rises above or drops below this range by more than 30 percent, the result is often lethal. So how does the body maintain control of its calcium?
As we've discussed in the past, the first thing you need to take control is a sensor that can detect what needs to be controlled. The cells of the four parathyroid glands that are embedded in the four corners of the thyroid gland have sensors that can detect the level of calcium in the blood.
The second thing you need to take control is something to integrate the data by comparing it to a standard, decide what must be done, and send out a message. When the calcium level in the blood drops, the parathyroid gland cells send out more parathormone (PTH) and when it rises they send out less PTH. Due to being broken down by enzymes, the metabolic effect of a given amount of PTH, like for most other hormones, only lasts several minutes, allowing the body to maintain moment to moment control.
The third thing you need to take control is an effector that can do something about the situation. The calcium blood level is determined by how much calcium moves in and out of the bone, how much is lost through the filtering of blood by the kidneys, and how much is brought into the body through the gastrointestinal system with the help of calcitriol (activated Vitamin D). Vitamin D is activated when the liver adds a hydroxyl group (OH) to its 25th carbon, followed by the kidney adding another one to its first carbon to produce calcitriol. If the kidney adds the OH to its 24th carbon instead, it results in an inactive form of Vitamin D.
PTH travels in the blood and attaches to specific PTH receptors on the bone cells and tells the osteoclasts to breakdown more bone to release more calcium and the osteoblasts to take in less calcium by making less bone. PTH also attaches to specific PTH receptors on the cells of the kidney tubules and tells them to take back more calcium from the urine that is presently in production. Finally, PTH attaches to specific PTH receptors on specialized cells in the kidneys and tells them to put OH on the first carbons of more 25 OH Vitamin D than on its 24th carbon, producing more calcitriol.
The combined effect of PTH is to increase the blood level of calcium by promoting its release from the bone, reuptake by the kidneys, and absorption into the body by the gastrointestinal system by increasing the production of calcitriol. When the blood level of calcium drops, the parathyroid glands send out more PTH to make the level rise back toward normal and when the level rises, they send out less PTH so it drops back toward normal. Due to the absolute need for the body to control its blood level of calcium, the absence of PTH or PTH receptors makes life impossible.
An abnormally high calcium level (hypercalcemia) is usually due to having too much PTH released by one or more of the parathyroid glands or widespread cancer. Since calcium is directly related to the development of bone, hypercalcemia can often result in weakening of the bone with increased pain and even fractures. Calcium also is connected with nerve function and hypercalcemia can cause anxiety, depression, and difficulties with concentration. This can progress to confusion, lethargy, coma, and death. Calcium is also important for heart function and hypercalcemia can cause rhythm disturbances and problems with heart function. However, one of the commonest problems encountered early on with hypercalcemia is the formation of kidney stones, because the increased blood calcium increases the amount of calcium in the urine, which can join with phosphate and come out of solution to form calcium phosphate crystals. This happens particularly when the person with hypercalcemia is dehydrated and is making very concentrated urine. For our earliest ancestors, this would have led to recurrent kidney infections and compromised kidney function.
An abnormally low calcium level (hypocalcemia) is usually due to low parathyroid gland function. This is often related to previous central neck surgery or radiation, severe Vitamin D deficiency, or chronic renal failure. Since calcium plays a major role in nerve and muscle function, the commonest early complaints of hypocalcemia are tingling and numbness of the hands and feet and around the mouth, in addition to muscle twitching and spasm. This can progress to seizures, difficulty breathing, and life-threatening cardiac rhythm problems.
The system the body uses to control its blood level of calcium requires calcium sensors on the parathyroid gland cells, the ability for these cells to produce PTH, properly adjusted release of PTH to the change in the calcium blood level, enzymes to limit the effect of PTH, and specific PTH receptors on the bone cells, tubule, and specialized cells of the kidneys. Without any one of these five components being present and doing what they're supposed to do, the whole system would fail and calcium control would be lost.
But for our earliest ancestors to have survived, like all other living creatures, not only would they have needed this irreducibly complex system but, in addition, it would have had natural survival capacity to make sure the blood level of calcium stayed within the right range. In other words, the systems the body uses must do the right thing at the right time and they must do these well enough to survive under the laws of nature. In any realistic perspective, this casts serious doubt on the idea that life came about by chance and nature's laws alone.

 

Inside Venezuela's mini apocalypse.

The fourth horseman rides on.

Why the talking primate is not just another ape.

Talk to the Animals? Yeah, Right
Tom Bethell 

We are frequently told that humans, mentally, are continuous with the apes. But it has always been an axiom, devoid of facts. Contrary evidence continues to grow. The latest case for a sharp division between us and the animal world was made by Alison Gopnik in her "Mind and Matter" column in the Wall Street Journal ("Adventures in Experimenting on Toddlers").

She illustrated it by posing this "small IQ test" for newspaper readers:

Suppose you see an experimenter put two orange blocks on a machine, and it lights up. She then puts a green one and a blue one on the same machine, but nothing happens. Two red ones work, a black and white combination doesn't. Now you have to make the machine light up yourself. You can choose two purple blocks or a yellow one and a brown one.

You figured it out, right? It's not any particular block that does the trick. Both have to be the same color.

"This simple problem actually requires some very abstract thinking," Gopnik adds. Toddlers as young as 18-to-24-months old "got it right, with just two examples." But other animals had "a very hard time" understanding it. "Chimpanzees can get hundreds of examples and still not get it, even with delicious bananas as a treat." (Chimps do have color vision, in case you were wondering.)

Conventional wisdom has been that toddlers can't learn this kind of abstract logical principle. Child psychologists such as Jean Piaget "believed that young children's thinking was concrete and superficial." Gopnik and her assistant now correct that, saying you have to watch what they do, instead of relying on what they say. Gopnik's article has now been published by the journal Psychological Science.

Ever since Darwin, the idea that there is nothing exceptional about humans has been an axiom of evolutionist thought.

Darwin wrote: "Man in his arrogance thinks himself a great work, worthy the interposition of a deity, more humble & I believe true to consider him created from animals." (See James Rachels, Created from Animals.)

Darwin's loyal followers, from T.H. Huxley to S.J. Gould and continuing today, have toed that line: We have all been deceived by our pride!

"Chimps and gorillas have long been the battleground of our search for uniqueness," Gould wrote in Ever Since Darwin. He went on:

For if we could establish an unambiguous distinction -- of kind rather than of degree -- between ourselves and our closest relatives, we might gain the justification long-sought for our cosmic arrogance. The battle shifted long ago from a simple debate about evolution: educated people now accept the evolutionary continuity between humans and apes. But we are so tied to our philosophical and religious heritage that we still seek a criterion for strict division between our abilities and those of chimpanzees.

The main evidence for an unbridgeable mental gulf between humans and animals comes from language. Children of a certain age (not too old!) can learn a new language practically overnight if they are moved to a foreign country. No one knows how it happens.

Numerous attempts to get young chimps to learn the language that small children easily learn have all failed. A detailed account could read like a comedy, but it would be irreverent -- to Darwinians -- so I shall refrain.

One chimp, Washoe, supposedly learned American Sign Language, but it may have been "confirmation bias." The feat could not be replicated by Nim Chimpsky. Watch the movie Project Nim, about the newborn chimp raised with humans. Nim Chimpsky was defiantly named after Noam Chomsky, the MIT professor who concluded that only humans have the ability to learn languages. Nim couldn't.

David Berlinski once heard Noam Chomsky say:

Every native speaker of a natural language is capable of producing and understanding infinitely many sentences that he has never heard or spoken before.

Chimps on the other hand, have never been able to speak a single sentence. We would never stop hearing about it if one had.

An expert on linguistics argued in 1975 that until man evolved a bent vocal tract he couldn't have produced vowel contrasts and therefore he didn't speak.

This was thought profound, another linguist (Noel Rude) added, "until somebody pointed out that parrots do quite well with just a beak."

The latest craze, with materialism our ruling dogma, has been to turn toward neuroscience. Chimp brains are so similar to human brains, that must be significant, right? Not really. It's the old homology argument, taken out for a new walk.

The claim of evolutionary continuity, made by Darwin, Gould and others -- based on our alleged vanity -- is not so much an argument as an accusation. In fact it is an assault on reason, for all along there has been strong evidence that humans are separated from animals not by a mutation but by a chasm.


Alison Gopnik's fascinating experiment only reinforces that.

Civil War VI

On the art of procastination.

On the global 1%

On origin of life science's and Darwinism's reproducibility issues

ASCB Addresses Problem of False Science

The Most Important Recommendation of All

The American Society for Cell Biology (ASCB) task force on reproducibility in life science research has issued an undated white paper on scientific rigor. The problem is, as we discussed here and here, life science research has been found to lack reproducibility. John Ioannidis is a bit more blunt as he explains that “most published research findings are false,” and that “claimed research findings may often be simply accurate measures of the prevailing bias.” The ASCB white paper is no doubt a step in the right direction. It offers 13 recommendations to encourage more rigor in training, publishing, and standards. But the most important recommendation of all continues to be ignored.

Daniel Sarewitz has noted not only the problem of bias in scientific research but also the causes. Note his final thought in this quote:

All involved benefit from positive results, and from the appearance of progress. Scientists are rewarded both intellectually and professionally, science administrators are empowered and the public desire for a better world is answered. The lack of incentives to report negative results, replicate experiments or recognize inconsistencies, ambiguities and uncertainties is widely appreciated — but the necessary cultural change is incredibly difficult to achieve.

And so it is that science’s much touted self-correcting, feedback loop which ensures science converges on the truth (after all, that’s what Mr. Wells told us in seventh grade science class) is sometimes a little slow to act.

And if the ASCB is still needing to remind scientists to clean their beakers and use checklists, imagine the difficulty in achieving more fundamental change?

This brings us to the recommendation that ASCB did not make—the most important of all. And that is for science to free itself of the excessive metaphysics. Unfortunately, progress on that front is glacial. As Sarewitz notes, one reason bias persists, and is so harmful, is that in the moment it is not perceived as bias. Asking an evolutionist to stop with the metaphysics goes nowhere because it isn’t recognized as metaphysics. Deep philosophy is a part of their “science” as much as red meat is a part of hamburgers.

Even if the ASCB task force members wanted to address this fundamental problem, they wouldn’t for the backlash would be overwhelming and their professional reputations would be ruined.

So while the pipettes will be sterilized and results double checked to the third decimal point, ASCB will continue to publish junk science driven by the Epicurean mandate that the world must have arisen spontaneously. Unfortunately, the ASCB task force has missed the most important recommendation of all.

Posted by Cornelius Hunter 

File under 'well said" XXVIII

Yesterday is ashes; tomorrow wood. Only today does the fire burn brightly. - 
 Inuit folk wisdom.

A clash of titans XX

It's design all the way down.

Organizer of body axes: 600 million years old molecular principles
Source:
University of Vienna

In humans and in animals, the correct position of tissues, organs and appendages is essential. Two body axes (the head-tail and the back-belly axes) usually define this position by generating a coordinate system, which supplies each cell in the body with its precise address. Thus, for example, the vertebrate central nervous system is always located on the back, and the intestinal tract on the belly of the animal.

In vertebrate early development, an "organizer" forms in the region of the primitive mouth (the blastopore) of the embryo. This organizer is responsible for guiding axis formation of the organism. Its discovery won Hans Spemann a Nobel Prize in 1935. The organizer tissue instructs the surrounding cells to take part in body axes development, enforcing a certain developmental fate on them. Without an organizer, the embryo would not know where the head, the tail, the back and the belly should be. Mistakes in the regulation of body axes can lead to severe developmental defects, for example to the formation of Siamese twins.

In the last 25 years, the researchers largely elucidated the genetic underpinnings of this very particular part of the vertebrate embryo. The widespread assumption was that the organizer was a specific vertebrate feature, since it was not readily observable in insect or worm embryos.

The team of Grigory Genikhovich and Ulrich Technau from the Department of Molecular Evolution and Development of the University of Vienna now demonstrated that not only the principle of the organizer but also its molecular underpinnings are much older than previously supposed. "By performing transplantation experiments and molecular analyses we have found a blastoporal organizer in the embryos of the sea anemone Nematostella vectensis. For inducing axes, it uses the same class of signaling molecules as the vertebrate organizer," explains Technau. "We conclude that this principle of the regulation of the embryonic axes existed already in the common ancestor of vertebrates and sea anemones more than 600 million years ago."

The lake of fire:The Watchtower Society's commentary II

LAKE OF FIRE

This expression occurs only in the book of Revelation and is clearly symbolic. The Bible gives its own explanation and definition of the symbol by stating: “This means the second death, the lake of fire.”—Re 20:14; 21:8.

The symbolic quality of the lake of fire is further evident from the context of references to it in the book of Revelation. Death is said to be hurled into this lake of fire. (Re 19:20; 20:14) Death obviously cannot be literally burned. Moreover, the Devil, an invisible spirit creature, is thrown into the lake. Being spirit, he cannot be hurt by literal fire.—Re 20:10; compare Ex 3:2 and Jg 13:20.

Since the lake of fire represents “the second death” and since Revelation 20:14 says that both “death and Hades” are to be cast into it, it is evident that the lake cannot represent the death man has inherited from Adam (Ro 5:12), nor does it refer to Hades (Sheol). It must, therefore, be symbolic of another kind of death, one that is without reversal, for the record nowhere speaks of the “lake” as giving up those in it, as do Adamic death and Hades (Sheol). (Re 20:13) Thus, those not found written in “the book of life,” unrepentant opposers of God’s sovereignty, are hurled into the lake of fire, meaning eternal destruction, or the second death.—Re 20:15.

While the foregoing texts make evident the symbolic quality of the lake of fire, it has been used by some persons to support belief in a literal place of fire and torment. Revelation 20:10 has been appealed to, because it speaks of the Devil, the wild beast, and the false prophet as being “tormented day and night forever and ever” in the lake of fire. However, this cannot refer to actual conscious torment. Those thrown into the lake of fire undergo “the second death.” (Re 20:14) In death there is no consciousness and, hence, no feeling of pain or suffering.—Ec 9:5.

In the Scriptures fiery torment is associated with destruction and death. For example, in the Greek Septuagint translation of the Hebrew Scriptures the word for torment (baʹsa·nos) is several times used with reference to punishment by death. (Eze 3:20; 32:24, 30) Similarly, concerning Babylon the Great, the book of Revelation says, “the kings of the earth . . . will weep and beat themselves in grief over her, when they look at the smoke from the burning of her, while they stand at a distance because of their fear of her torment [Gr., ba·sa·ni·smouʹ].” (Re 18:9, 10) As to the meaning of the torment, an angel later explains: “Thus with a swift pitch will Babylon the great city be hurled down, and she will never be found again.” (Re 18:21) So, fiery torment here is parallel with destruction, and in the case of Babylon the Great, it is everlasting destruction.—Compare Re 17:16; 18:8, 15-17, 19.


Therefore, those who are ‘tormented forever’ (from Gr., ba·sa·niʹzo) in the lake of fire undergo “second death” from which there is no resurrection. The related Greek word ba·sa·ni·stesʹ is translated ‘jailer’ in Matthew 18:34. (RS, NW, ED; compare vs 30.) Thus those hurled into the lake of fire will be held under restraint, or “jailed,” in death throughout eternity.—

Jesus v.the Pharisees re:ceremonial purity the Watchtower Society's commentary.

Why was handwashing an issue for Jesus’ antagonists?

This was just one of many issues in which Jesus’ enemies found fault with him and his disciples. The Mosaic Law included a number of commands on ceremonial purity regarding such matters as bodily discharges, leprosy, and dealing with human and animal corpses. It also gave instructions on how impurities could be removed. This could be done by sacrifice, washing, or sprinkling.—Lev., chaps. 11-15; Num., chap. 19.

The Jewish rabbis expounded on every detail of these laws. One source says that each cause for impurity would be subjected “to questioning concerning the circumstances in which it may be contracted, how and to what extent it may be transmitted to others, the utensils and objects capable and incapable of becoming unclean, and finally, the means and rituals required for purification.”

Jesus’ opponents asked him: “Why do your disciples not observe the tradition of the men of former times, but they eat their meal with defiled hands?” (Mark 7:5) Those religious enemies were not referring to the taking of sanitary measures. As a ritual, the rabbis required that water be poured over their hands prior to eating. The above-quoted source adds: “It is also debated which vessels are to be used for the pouring, which kind of water is suitable, who should pour, and how much of the hands should be covered with water.”


Jesus’ reaction to all these man-made laws was simple. He told the first-century Jewish religious leaders: “Isaiah aptly prophesied about you hypocrites, as it is written, ‘This people honor me with their lips, but their hearts are far removed from me [Jehovah]. It is in vain that they keep worshipping me, for they teach commands of men as doctrines.’ You let go of the commandment of God and cling to the tradition of men.”—Mark 7:6-8.