Apr 11 2014

Should you circumcise your child?

Probably not. But the New York Times reports:

A review of studies has found that the health benefits of infant male circumcision vastly outweigh the risks involved in the procedure.

Actually, it doesn’t. Not at all. The paper is all about the frequency of circumcision in the US; this is the only real data in the paper, and notice that a good chunk of it is speculation.

Prevalence of adult circumcision in the United States during the past 6 decades (1948-2010). The solid line represents documented prevalence among adults; dashed line, [Morris's] predictions.

Prevalence of adult circumcision in the United States during the past 6 decades (1948-2010). The solid line represents documented prevalence among adults; dashed line, [Morris's] predictions.

It does toss in a table purporting to show the tremendous risks of not circumcising baby boys, but this is not new — these are the same sloppy data that the author has been peddling for over a decade. With some trepidation, I give you a sample from his 2007 paper: don’t trust these numbers!


The author is Brian Morris, better known as the Man Who Hates Foreskins. He’s a real crusader, who touts foreskin removal as just as important as vaccination — that leaving it intact imperils the child to a 1 in 3 chance of a serious condition requiring medical attention. You might immediately question how he arrives at this conclusion — by multiplying a series of dubious assertions together — and the likelihood of it being true, given that circumcision is a culturally variable practice, and that countries where it’s rare (for instance, in Scandinavia, where the frequency of circumcisions is around 2%) don’t typically have emergency rooms crowded with young boys whose penises are in painful, infected, states, raddled with disease.

I suppose it could be because glorious Scandinavian penises are perfect and universally wholesome — that’s what I’ve been told, anyway — but that would be baseless speculation and unwarranted extrapolation of anecdotes into unsupportable evidence, of the sort that Brian Morris does.

Take that first condition, the likelihood of urinary tract infections. That’s taken from a sample of 36 children, half of whom had an unknown circumcision status, and the difference was not found to be statistically significant. Yet here he just presents it as established fact, that uncircumcised children have a ten-fold greater rate of urinary tract infections.

Or look at his claim of much greater rates of HIV infection. There actually is some interesting mechanistic reasoning behind that: the foreskin represents an enlarged area of delicate membrane which could be an avenue of entry for some viruses. But the real test would be an epidemiological study: there are lots of circumcised men around, and lots of uncircumcised men, when we look at the rates of infection, is there a significant difference? It hasn’t been done very often, but when it is, the hypothesis often fails to be supported. Here’s one example of a scientist who thought heightened sensitivity to STIs was a reasonable hypothesis (his “hunch”), but found it didn’t pan out at all when examined.

Armed with this hunch, rather than set up a website I chose to do some research. Australia is a good place to do such research because there is a roughly even population split for the intervention (circumcision) and in most cases it is not a maker of ethnicity, wealth, education or religion. Unexpectedly, our research findings were uniformly negative. Circumcision did not protect against STDs in our clinic population, though we did not look at HIV because it is rare in heterosexual men in Sydney.

Then there are some of Morris’s very peculiar ideas. This is the abstract from a paper advocating more circumcision; note that one of his arguments is basically that women find uncircumcised penises ugly. As usual, no evidence for that is presented.

Circumcision of males represents a surgical “vaccine” against a wide variety of infections, adverse medical conditions and potentially fatal diseases over their lifetime, and also protects their sexual partners. In experienced hands, this common, inexpensive procedure is very safe, can be pain-free and can be performed at any age. The benefits vastly outweigh risks. The enormous public health benefits include protection from urinary tract infections, sexually transmitted HIV, HPV, syphilis and chancroid, penile and prostate cancer, phimosis, thrush, and inflammatory dermatoses. In women circumcision of the male partner provides substantial protection from cervical cancer and chlamydia. Circumcision has socio-sexual benefits and reduces sexual problems with age. It has no adverse effect on penile sensitivity, function, or sensation during sexual arousal. Most women prefer the circumcised penis for appearance, hygiene and sex. Given the convincing epidemiological evidence and biological support, routine circumcision should be highly recommended by all health professionals.

I suspect that women’s preferences are going to be shaped by culture, by familiarity, rather than some objective hideousness of the foreskin, and what the heck is appearance doing in a paper that is supposed to be summarizing medical evidence, anyway?

It’s also an argument that can cut both ways. When presented with evidence that one phenomenon, dyspareunia (painful intercourse) was found to be more common in partners of circumcised men than uncircumcised men, Morris waved it away by arguing that women in countries with lower rates of circumcision might be disturbed by the sight of a cut penis.

Morris et al. should be commended for their creative attempt to dismiss the higher prevalence of frequent dyspareunia in women with circumcised (12%) than uncircumcised (4%) spouses (ORs between 4.17 and 9.00). They suggest that Danish women with circumcised spouses may be so psychologically troubled by the shape of their spouse’s penis that it might result in painful intercourse. A more plausible explanation would be that reduced penile sensitivity may raise the need among some circumcised men for more vigorous and, to some women, painful stimulation during intercourse in their pursuit of orgasm.

But then, that’s Brian Morris all over the place. He actively tries to suppress work that doesn’t support his conclusions, he inflates any evidence that suggests circumcision might have a few benefits (there are some!), and dismisses any evidence to the contrary…or worse, twists it around to claim it supports the opposite of the author’s interpretations. All this in defiance of worldwide statements from pediatric organizations that say the evidence for health benefits from circumcision are weak, and that routine circumcision is not recommended.

One other weird thing: why are circumcision advocates so obsessed with this procedure? It’s certainly not that the benefits are as solidly established as they are for vaccination; reading the literature, the most striking observation is the murkiness and insignificance of the evidence. If you’ve got lots of studies, and they vary up and down in their conclusions, and are constantly skirting the margins of likelihood, what’s the best explanation: that there is a strong effect that can only be detected by true believers, or that we’re dealing with no effect at all and people are cherry-picking peaks and troughs from statistical noise? I lean towards the latter. The former is also the excuse used by psychics, UFOlogists, and Bigfoot hunters.

It also doesn’t help that Morris has been affiliated with the Gilgal Society a pro-circumcision organization that also published a book of ‘erotic’ circumcision stories.

Yes, you read that right. Circumcision child porn. Short excerpt below, in rot13.

Ur unq abg ernpurq choregl ohg fbba jbhyq: n srj unvef jrer fgnegvat gb tebj ng gur onfr bs uvf cravf. Arvy jnf gura nfxrq gb yvr ba gur pbhpu sbe gur cravf gb or cubgbtencurq. …gur qbpgbe grfgrq gur svg bs gjb fvmrf bs Tbzpb Pynzc oryy. Qhevat guvf cebprqher Arvy rerpgrq, ohg jnf abg rzoneenffrq ol vg naq znqr ab nggrzcg gb uvqr vg.
Znex pnzr va arkg naq ntnva qebccrq uvf gebhfref ernqvyl. Ur unq ernpurq choregl naq jnf dhvgr jryy qrirybcrq. … Vgf yvxr na ryrcunagf gehax jnf gur qbpgbef pbzzrag, gb juvpu Znex urnegvyl nterrq. … Cubgbtencuf bs uvf cravf jrer gnxra…
Ur unq ernyvfrq nsgre frk rqhpngvba yrffbaf ng fpubby gung ur unq n ceboyrz.
…gur oblf jrer tvira cyragl bs jvar gb erynk gurz. …gur qvfphffvba jnf nobhg gur frk yvirf bs gur oblf naq gurve fpubby sevraqf. Gur qbpgbe nfxrq ubj bsgra gur oblf jnaxrq. … Gur qbpgbe fubjrq gur oblf uvf zvpebfpbcr naq nfxrq vs gurl unq rire frra fcrez haqre bar. … Ur fhttrfgrq gb Znex gung vs ur jnagrq gb, ur pbhyq unir n dhvrg jnax juvyfg Arvy jnf orvat pvephzpvfrq… Guvf jnf rntreyl npprcgrq. … Ur ynl onpx jvgu uvf rlrf pybfrq naq whfg yrg gur qbpgbe trg ba.

Morris has been trying very hard to dissociate himself from Gilgal, at least, but still…eww.

“Gilgal”, by the way, is apparently Hebrew for “hill of foreskins”. Really? They needed a word for that? Double eww.

Frisch M (2012) Author’s Response to: Does sexual function survey in Denmark offer any support for male circumcision having an adverse effect? Int. J. Epidemiol 41 (1): 312-314.

Morris BJ (2007) Why circumcision is a biomedical imperative for the 21st century. Bioessays 29(11):1147-58.

Morris BJ, Bailis SA, Wiswell TE (2014) Circumcision Rates in the United States: Rising or Falling? What Effect Might the New Affirmative Pediatric Policy Statement Have? Mayo Clin Proc doi: 10.1016/j.mayocp.2014.01.001. [Epub ahead of print]

Apr 11 2014

Condescending Republican compares abortion to buying new carpeting for his car

Chuck Gatschenberger wants to have a mandatory 72 hour waiting period before a woman is allowed to have an abortion…and his argument by analogy is that when he visits a car dealership, he doesn’t impulsively buy a car or recarpet his old one.

House Bill 1613 would require an ultrasound and also triple Missouri’s mandatory waiting period for a woman seeking abortion to 72 hours. Gatschenberger suggested that his legislation would make a woman "research" her decision before having an abortion — a move he said would increase the odds that she will choose life for her unborn baby.

That’s so sweet. So is House Bill 1614 going to require a 72 hour waiting period for all car purchasing decisions? Just think how poor Chuck would feel if he went into the car dealership and discovered he’d have to wait three days on anything.

But don’t worry, he has “apologized”.

Gatschenberger apologized for offending the women in the room and said his intention was simply to ensure that women considered their reproductive decisions more carefully.

“I’m just saying this is a life-ending decision,” he said. “You should think about it.”

Because women just never ever think before they rush off to get a surgical procedure. Flighty, stupid women — they all need a man to help them with these decisions.

Apr 11 2014

Friday Cephalopod: Octopuses can be superheroes, too

Apr 11 2014

Troll policy discussion

We’ve been getting persistently trolled by one person over the past month. Remember krooscontrol? How about Tomas C? chaoticinflation? All the same person. He has a couple of tells that make him easy to detect once I picked up on them. That latest incarnation, chaoticinflation, is now banned, but if his past record is any guide, he’ll invent a new pseudonym in the next day or two and be right back at it, so if you see any familiar arguments emerging from some new person who just popped up, let me know.

I have a few questions to discuss, though.

One, why are these people who show up to argue for godly objective morality so consistently unable to represent honesty and forthrightness? I’m thinking it either means their god is a lying sleaze who left those traits out of his list, or more likely, that being a dishonest coward is a prerequisite for being a fanatical Christian. They aren’t showing their faith in a good light, that’s for sure.

Two, as a matter of policy, I’ve had zero tolerance for people who show up under false pretences: if you’ve been banned and then leave comments under a sock puppet account, I delete those entries. There should be no reward for evading our rather simple mechanisms to filter out bad actors — really, any idiot can do it, as all the idiots have demonstrated. Unfortunately, this bozo has left over 600 comments here.

Think about that. This obsessed kook has shown up here to lie at us about 20 times a day. The boy has fuckin’ problems.

Now I’ve got all those comments queued up in a list — I told you, there are some easy searchable tells — and I could just click the button to select them all, then click “delete”, and they all get flushed. I know some of you don’t particularly care to see gaps that big appear in threads, so I’m holding off for now. You tell me: flush the crap or let it stand?

OK, people, one thing will not change: when some demented asshole like Graeme Bird shows up, spews a lot of garbage that includes outright racist/anti-semitic slime, I will delete it. No question. No hesitation.

I know it’s hard when the lunacy is so extreme it becomes comedic, and it’s also hard when the wretched racist just dumps a swarm of comments (Bird commented 73 times last night), but try to resist. Now all of your comments are left dangling without referents.

Apr 10 2014

Kilstein is in flyover country

Just a reminder that tomorrow, Friday evening, Jamie Kilstein will be performing at Freethought Festival 3 in Madison, WI. This video is definitely NSFW, but it’s hilarious.

I am tempted to just hop in my car and make the 7 hour drive to Madison…but I’m going to be trapped in grading all weekend instead. I do not want to be a grown up anymore.

By the way, he makes a good point that I’ve noticed, too. Piss off the Catholics, they’ll swarm you with letters accusing you of persecuting them, with lots of “I’ll pray for you” noise, and only an occasional death threat. Piss off the anti-feminists, especially the sexist atheists, and you will get real rage-hate of a magnitude I never saw from the Christians. It’s actually the most appalling and disappointing failure of movement atheism, its failure to strongly support equality.

Apr 10 2014

The poor are lazy, the rich are selfless, says Ben Stein

I had almost forgotten that Ben Stein existed — Expelled seems to have been the last sad gasp of his marginal cinematic career. But he still lives on, whining on the virtual pages of wingnut webzines like The American Spectator. His latest is a discussion of all that is wrong with poor people.

My humble observation is that most long-term poverty is caused by self-sabotage by individuals. Drug use. Drunkenness. Having children without a family structure. Gambling. Poor work habits. Disastrously unfortunate appearance. Above all, and counted in the preceding list, psychological problems (very much including basic laziness) cause people to be unemployed, have poor or no work habits, and enter and stay in poverty.

Impoverished people have personal problems. They may have had terrible childhoods. They may have been the victims of abuse. They are often the victims of their own abuse of drugs and alcohol. But they are not the victims of corporations or of the Federal Reserve. Their sad backgrounds lead them into self-destruction.

It is all their own damn fault. Also, they aren’t actually poor, because they have indoor plumbing. How can they be complaining about their situation if they’ve got a working toilet?

Meanwhile, rich people are good.

But there are just some people who are better with money than others and will wind up with a ton of money. There will be people who strike oil, who create new Internet toys. They fund symphonies and ballets and schools for inner city kids. They are a bulwark against tyranny because they can afford lawyers to fight overweening government.

We want for there to be a high number of rich people who function as a brake on government just as the nobles did on the crown in long ago England.

They fund symphonies! Without rich people of good taste, all those inner city kids might have to listen to is that godawful rap crap, you know. Rich people have a mission to dictate taste as well as to set an example for the poors.

Why is it that I think that the rich are paying lawyers not to fight for equality and fairness and justice, but mainly to make sure that they don’t have to pay as many taxes as they should?

Don’t warry, though, Ben Stein has a solution.

What will make the genuinely poor stop sabotaging themselves? Maybe, just maybe, if we let God back into the public forum it would help. I have seen spiritual solutions work miracles.

Jebus. What an idiot.

Apr 10 2014

Plastic: worse than we thought

That plastic grocery bag you got at the store is something more than just an eyesore and a source of nasty chemicals, it’s also a magnet for accumulating more pollutants.

The ingredients that make up more than 50% of plastics are already deemed chemical hazards by the UN Globally Harmonized System. But as floating bits of trash, plastics pick up additional pollutants like pesticides, flame retardants and combusted oil. “We don’t know yet how long it takes plastic to fully break down, but it’s somewhere on the order of tens to thousands of years,” says Rochman. This means that plastic debris accumulates a multitude of toxic chemicals over potentially many, many years. This type of marine plastic is ending up as lunch for birds, fish and other animals.

The article goes on to detail specific effects of PAHs, PCBs, and PBDEs on medaka. It’s ugly. Now I just have to figure out a way to reduce plastic consumption at home — it’s painful how much of our food and other essentials are packaged up in plastic.

Apr 10 2014

Bringing back Salt Lake memories

In anticipation of the American Atheist conference next week, many ex-Mormons marched and sent in resignation letters to the LDS leadership. The timing was key.

David Silverman, president of the American Atheists, said the Mormon church has too much influence on people’s lives, especially Utahns’. Officially leaving the church during General Conference sends a message, he said.

"They’re doing it during the General Conference to make a statement, and that statement is that they feel oppressed here in Salt Lake City, where the Mormon church governs so much of not just the Mormons’ lives but everybody else’s lives," Silverman said. "It’s not fair. It’s a violation of the separation of church and state, but it’s also a violation of religious freedom."

They did it during the General Conference? Risky. It might have gotten completely ignored.

When we lived in Salt Lake City, I remember the General Conferences as the times when a news blackout fell over the state. The local newspapers would all run big front page stories on the most tedious pablum: “SENILE OLD MAN SPEAKS FOR TWO HOURS ON HOW WE SHOULD BE NICE”. The LDS leadership was (is) all these older conservative fellows in the same dark suits who took themselves very seriously, and all the news organizations were expected to report in detail everything that was said…not that they ever said anything of any interest or importance whatsoever. It was the time of the year that felt closest to living in North Korea — although, of course, the LDS church never subscribed to purging undesirables with flamethrowers. No violence, just state-enforced veneration of the blandest boringest bureaucrats of the church.

Most of the time, you could ignore the Mormon leadership, especially if you were living in SLC, which was about half Gentile. Not during the General Conference. Even then, though, what was most striking wasn’t the actual leadership, which was facelessly tedious, but that there were so many devout Mormons who would reverently worship every word dripping from the White Geezers at the top. It was weird; it was the time of year when the pod people would start speaking synchronously.

Apr 09 2014

Another free conference this weekend

I guess it’s that time of year — the Freethought Festival is taking place in Madison this weekend. Go!

Third Annual Freethought Fest To Draw Crowd This Weekend

The UW-Madison student organization Atheists, Humanists, and Agnostics is holding their third annual Freethought Festival this weekend, set to take place at two venues in Madison, WI. The Freethought Festival is a free, student-run secular conference held annually in Madison, Wisconsin. Authors, bloggers, activists, and scientists from around the country come to speak on secular and scientific issues.

The event’s headliner is Dan Savage, the prominent gay rights and atheist who
founded the It Gets Better Project and creator of the “Savage Love” advice column and podcast.

Freethought Fest will also include a debate between Dan Barker, the Co-President of the Freedom From Religion Foundation, and Matt Slick, the President of Christian Apologetics and Research Ministry, on the subject “Does God Exist?”

“Freethought Festival will give the spotlight to many prominent atheists who are making positive differences in the world,” AHA President Sam Erickson said in a statement. “It will be exciting to be a part of that and hear all of the speakers share their experiences and perspectives.”

Along with Barker and Savage several atheist activists will speak, including comedian Jamie Kilstein, fellow Co-President of the Freedom From Religion Foundation Annie Laurie Gaylor, parenting expert and author Dale McGowan, three-­time Emmy winner Jay Rosenstein, and blogger/author Hemant Mehta.

Freethought Fest is open to everybody, free to attend, and has a predicted attendance rate of approximately 1,100.

AHA is one of the largest atheist college groups in the world, and is proud to provide a safe space to nonreligious people on campus where they can express themselves and connect with other nonbelievers, while promoting the discussion of religion on the UW-Madison campus.

“We wanted to create an event that would enrich the UW Campus and inform as well as entertain members of the UW Community,” Erickson said.

The event is funded by AHA through an annual operations budget received from the University of Wisconsin-Madison. AHA is proud to put on an event that will draw a wide range of attendees from the UW community while promoting freethought, secularism, and skepticism.

For more information, please visit freethoughtfestival.org

Apr 09 2014

No! Not the list of stumpers again!

There’s a common tactic used by creationists, and I’ve encountered it over and over again. It’s a form of the Gish Gallop: present the wicked evolutionist with a long list of assertions, questions, and non sequiturs, and if they answer with “I don’t know” to any of them, declare victory. It’s easy. We say “I don’t know” a lot.

Jack Chick’s Big Daddy tract is a version of the creationist list, and contains a fair amount of fantasy as well. You know what they believe will happen: they’ll ask that one question that the scientist can’t answer, and then they’ll have an epiphany, a revelation, and realize that all their science is a lie, at which time they’ll resign from their university position and join a good bible-believin’ church.

It happens to me all the time, too. At one talk I gave, there was a woman at the door who had printed a 5-page, single-spaced list of questions, and she was telling everyone going in to ask me to answer them — I invited her to come in and listen to the talk and ask them herself, and she ran away. I’ve had a Canadian creationist do the same thing, and then I talked to him for several hours in the hallway after the talk. He seemed stunned and angry that I actually had answers for most of his questions. I have been confronted by people with questions (more like ignorant assertions) about biology, who once I’ve answered them and reveal that I’m a biologist, switch to asking me about geology and the Big Bang, to get me into a corner where I’d have to say, “I don’t know.”

Here we go again. The IDiot, Salvador Cordova, has written up his list of 16 questions to challenge scientists. He even has the typical anecdote:

I once gambled a little bit on a weaker question that a creationist biology student should ask her anatomy and physiology professor regarding the evolution of hearts. I basically suggested she ask about how the intermediate plumbing can work if it is not all wired-correctly in the first place.

When that biology junior posed that question, she came back the next week at our ID/Creation meeting beaming. She said, “you’re right, there are no transitionals!” I realized then whatever I said might not be as powerful as what professors are unable to say when asked the right questions!

But we do have intermediates, both phylogenetically and developmentally! People are using zebrafish to study the evolution of the four-chambered heart. How can you conclude that there are “no transitionals” from one question about one feature, asked of one professor? But that’s exactly the illogical conclusion creationists want you to draw.

Here’s how the scam works and gives them the answers they want.

  • Ask questions about wildly different fields: Cordova’s list includes questions about biology, geology, and cosmology. There are few people polymathic enough to know them all; I can handle most biology questions comfortably, but I have to beg off on geology and physics, or give general answers built on the lay knowledge I have of those fields. “I win!” declares the creationist, because Myers hasn’t memorized all the transitions in nucleosynthesis.

  • Ask about obscure phenomena within the evolutionist’s own field. No, I haven’t tracked every fossil discovery in the world; no, I haven’t memorized every signaling pathway; no, I don’t have a complete, step-by-step explanation for the evolution of every molecule in your body. I can look it up later, or I can give you an example of a related phenomenon, but that’s taken as an admission of failure of the whole field of biology, rather than an admission of my personal, limited competence.

  • Rely on the fact that not everyone pays attention to the basics. Most scientists are specialists; we’ve got a narrow set of topics that we know exceedingly well, and a great cloud of generalities that we sort of vaguely accept. Nobel prize winners are rarely the best people to consult about the kinds of things creationists want to know; for that, you’re better off talking to the academic grunt who teaches introductory biology, or the person who has a hobby of following the creationist literature (hey, that’s me!).

  • Ask really stupid questions. They misuse jargon, babble about facts that have been strongly established as if they’re controversial, throw in random bits of sciencey terminology that aren’t actually relevant to the question, but sound impressive to lurkers who are as ignorant as they are. The goal is to get the scientist to screw up their face in a “WTF?” expression, and go silent for a few minutes as they try to puzzle out a diplomatic way to shoo the time-wasting creationist away. That counts as scoring a coup.

  • Lie. Lie, lie, lie. Nobody in the audience will care to double-check creationist claims, except the scientists, and by the time they write up a detailed rebuttal, the creationist will have moved on to the next sucker.

So let’s take a shot at Cordova’s questions. I’ll just fire back as I would in person, without looking things up in a textbook or the internet.

1. How can functional proteins form without ribosomes or ribosome-like machines?

Ribosomes are great big elaborate enzymes…that is, they’re catalysts that enhance the rate of a reaction that would occur naturally. Without ribosomes, you’d still get short peptides forming; to get long ones, you’d need efficient catalysts to get the sequence to be assembled with high probability in a reasonable period of time. Early life would have been relatively inefficient, but they only had to compete with other protocells without the advantage of ribosomes.

2. How can natural selection or neutral evolution evolve poly constrained DNA or any poly constrained systems in general?

Classic use of jargon, “poly constrained”, to pretend the problem is a serious scientific one. An enzyme might be constrained in its sequence at multiple points — it needs a specific amino acid at the active site, it needs another amino acid at a specific point to put a particular kink in the shape, it needs yet another specific amino acid at a distant point to interact with a regulatory protein — but that just means substitutions at those locations will occur at a lower rate and have fewer degrees of freedom than other locations.

3. How did the first organism regulate protein expression and cellular development without regulatory elements or developmental mechanisms?

Define “first organism”. Sufficiently primitive protocells probably didn’t regulate everything — they may have produced an enzyme for substrate X even when substrate X wasn’t present. So? But you can also see how, in an organism like that, there would have been a selective advantage to organisms that had a sensor to detect the presence of a substrate, allowing them to conserve a little energy by not producing the unnecessary enzyme. And the word “sensor” is used generously here: it would just mean a protein that could undergo a conformational change when bound to the substrate, and since it has an enzyme that binds the substrate already, it wouldn’t be difficult to evolve.

4. How did any vital organ or protein form given the absence of the organ would be fatal? Absence of insulin is fatal in organisms requiring insulin. How did insulin become a vital part of living organisms? If you say it wasn’t essential when it first evolved, then how can you say selection had any role in evolving insulin without just guessing?

This sounds like a clumsy version of irreducible complexity, which has already been shot down many times before. The organ/protein would not have been vital essentially, but could still have been useful. Look at Thornton’s work on the evolution of receptors: a broad spectrum corticosteroid receptor evolved into two much more specific glucocorticoid and mineralocorticoid receptors. The function only became essential after it was fully integrated into the physiology of an organism.

5. How did DNA evolve in a proteins-first or RNA first scenario?

You do know that the difference between DNA and RNA is simply the presence or absence of a single hydroxyl group, right? Once you’ve got the machinery to build and assemble ribonucleotides, it’s a short step to deoxyribonucleotides.

6. How did amino acid homochirality evolve since the amino acids in biotic soup experiments are racemic, plus homochiral amino acids spontaneously racemize outside of living systems? How about DNAs and sugars? If the expectation value is 50% left, how do 100% left or right forms emerge in pre-biotic soups, and more importantly how is homochirality maintained long enough for chemical evolution to work?

Enzymes are chiral, too. To maintain the synthesis of racemic products, you’d often need two different enzymes. To produce just one chirality, you need one kind of enzyme. Which is easier, to evolve one enzyme, or to evolve two simultaneously, one of which is a mirror image of the other?

7. Don’t dead dogs stay dead dogs and doesn’t Humpty Dumpty stay broken?

I don’t even…

There’s a bit of a difference between incremental assembly of the components of a dog over billion years, where each step is viable and subject to selection, and the instantaneous assembly of a complete dog from a non-viable collection of rotting organic compounds.

8. Describe how a partially functioning ribosomes or any partial implementation of the DNA code could operate in a working cell, and how a such cell can operate without such vital parts.

Didn’t we already address that in #1?

9. Are most laboratory and field observations of evolution reductive rather than constructive of new coordinated functions? For the sake of argument, let extinction can count as reductive evolution. When bacteria evolve antibiotic resistance, what proportion of cases involved evolution of a new complex protein?

Answer to the first part: no. If extinction is “reductive evolution”, then speciation is “constructive evolution”.

Second part: quantitatively, I don’t know. Almost certainly very low. Evolution is largely going to proceed by modification of existing components, and de novo creation of a complex protein is unlikely.

10. Cite an experiment or field observation where a substantially new protein was evolved in real time or is expected to evolve in real time over the next few generations. Nylonase is the most cited example, but that wasn’t a substantially new protein. But even granting that, how many complex proteins are evolving in the biosphere versus those getting lost forever.

Wait, why are you ruling out nylonase? It is a new protein! I notice you’re hedging your question, asking for a “substantially” (quick, define it) new protein, which has to evolve in “real time”, whatever that is, and right away you’re excluding obvious examples. What’s the point of answering this if you’re going to set it up with weasel words and exceptions?

All of the complex proteins in the biosphere are evolving. Since the number of genes in animals, to use one subset, wobbles about in different species but is staying in the same ballpark for the last few hundred million years, I’d have to estimate that gene losses are roughly equal to the addition of new genes.

11. What new trait in human populations do you expect to become genetically fixed in all 7 Billion or so people, and how fast do you expect that trait to overtake the population in how many generation? If you can’t identify convincingly one or a few traits, how then can you argue for evolution of so many traits in the past?

You’re asking me to do something that evolution does not claim to be able to do: evolution is not deterministic, involves a great deal of chance, and even selection is contingent on interactions with a changing environment, so it is impossible to predict the future fate of a single allele.

We can see it retroactively. A third opsin gene arose early in primates, and is basically now fixed in the human population, giving us trichromatic vision; we’re seeing lactose tolerant variants arising in humans within the last 10,000 years, not reaching worldwide fixation yet, but rising in frequency rapidly. That one could reach fixation, if dairy products become universally available and popular.

12. If a species has a population of 10,000, how can selection act in a particulate manner on 4 giga bases of DNA individually? Wouldn’t such a large genome relative to small population size result in lots of selection interference, hence wouldn’t most molecular evolution be neutral of necessity as Kimura asserted?

Most molecular evolution is neutral. Done.

13. Do geological layers involving permineralized fossils or other kinds of well-preserved fossils require rapid burial? If the burial process is rapid, does it really take millions of years then to make that particular layer that has fossils? If you find C14 in Cambrian fossils not the result of contamination or lab error, does that mean the fossil had a more recent time of death than 500,000,000 years? Given the half lives of DNA and amino acids or other decay processes of biological organisms, how can we account for preservation of these biotic materials for far longer than indicated by their chemical half-lives?

Now we get into geology and physics, outside my domain of expertise. I would either pull a convenient expert into the conversation, or admit I can only speak in generalities at this point. I would say, for instance, that 14C is produced by the interaction of high energy particles with nitrogen, so we wouldn’t expect it to be simply zero in all ancient specimens — just much, much lower than the amount produced by high altitude cosmic ray interactions with our atmosphere. Also, the life of an organic chemical is going to be dependent on the presence of other chemicals in the environment. It’s not going to be clocklike, like radioactive decay.

14. Can geological strata form rapidly? What about the university experiments and field observations that show strata can form rapidly? If they can form rapidly, and if fossil presence demands they form rapidly, doesn’t that suggest they formed rapidly?

What do you mean by “geological strata”? I think you mean just layers. Layers can form rapidly or slowly. They can be modified by processes that take long periods of time, and geologists look at the totality of the events that led to the feature they’re looking at. I’d say your question is very silly and it sounds like you’re about as ignorant of geology as I am, or worse, so talk to a geologist.

15. If redshifts in the Big Bang model are discovered to be possibly caused by other mechanisms than relative motion, wouldn’t that put the Big Bang in doubt? Wouldn’t that also raise questions about stellar distances?

Physics now? There is much more evidence for the Big Bang than just redshifts. Talk to a physicist. Are you seriously trying to suggest that the stars are significantly closer than has been measured by, for instance, parallax? Is this a question about the age and size of the universe? Because you’re really drifing into abysmally stupid territory here. Would you also like to argue that the sun orbits the earth and that the earth is flat?

16. What is the farthest astronomical distance that can be determined by parallax or very long base line interferometry, and what fraction is that detection distance relative to the claimed size of the visible universe relative to the Big Bang? How do you account for Super Nova by stars not inside galaxies? If so, doesn’t that mean there is a higher probability of Super Nova in a star outside a galaxy by a factor of hundreds of billions if not more? If so, why should this be?

I am not an astronomer, but I do happen to have a vague idea of the answer to the first question: it depends entirely on the accuracy of the instrument used to measure parallax. I think we’ve got parallax measurements out to around 500 light years? I’m sure an astronomer will correct me.

This question is so far outside my field I’m more curious to know what your intent in asking it might be. Are you really playing at being an intelligent design creationist, and are actually a young earth creationist at heart? Are you really bothered by the immensity of the universe, and are desperately trying to justify shrinking it down…happily contradicting all the physical evidence? How small does the universe have to be to make you content?

Ah, well. That’s Salvador Cordova for you. I think he’s competing with Casey Luskin for the title of Dumbest ID Creationist of Them All.

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