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Off the Top of My Head

The Code Breaker

by John Lawrence, March26, 2021

The Code Breaker by Walter Isaacson is an exciting new book which details the efforts and the knowledge to edit genes known as CRISPR. That means cutting into the DNA genome and removing "sick" genes and/or replacing them with the correct genes. The book details the quest to discover the mechanism by which this is possible. The book focuses on Jennifer Doudna but many researchers, many of them recent immigrants or workers at foreign universities, are involved. The fundamental insights can be explained in a few sentences. They noticed that bacteria have been fighting off viruses successfully for billions of years, and they were doing this by incorporating the virus DNA into the data base of their own genome. Upon encountering a new virus the bacteria knew how to encode that virus's DNA so that they could identify it in an attack in the future. Secondly, the bacteria knew how to dispatch a portion of RNA that would travel to the site of the virus and encode an enzyme that would then destroy the virus. The messenger RNA knew precisely where to point the enzyme which then cut the virus DNA thereby destroying it. So the e. coli bacterium has known how to edit genes for billions of years. The trick is to figure out exactly how the bacterium does this.

So Jennifer Doudna and cohorts did just that: They figured out how a bacterium cuts a virus's DNA precisely in a certain location. That's what the book is about. That's what gene editing is about. Gene editing is in its infancy, but it has already been used to correct the genetic mutation which causes sickle cell anemia which is caused by the mutation in one gene. Experimentally, it has been shown that if this gene can be cut out and replaced by one that contains the correct genetic information, the disease can be cured. If this can be done early in the development of an embryo, the correct gene can even be transmitted to succeeding generations. An estimated 8 million children are born each year with severe genetic disorders or birth defects. Gene editing can possibly correct some or all of these defects. In order to do this the enzyme which cuts the gene out of the DNA must be told precisely where to cut, and the correct gene must somehow be implanted precisely at this location and the DNA reconnected. In theory the whole idea is very simple. Figuring out how to do this either in the laboratory or in actual animals, much less in humans, is the hard part.

Whether or not this research will lead to an understanding of the origins of life is an open question. Perhaps there is a sub-atomic entity sort of like a neutrino which is massless and ubiquitous in the universe which is the progenitor of life wherever conditions are propitious. Perhaps it is able to generate an organism with the minimal genome, something which has never been discovered in nature. Even a virus which has the simplest known genomic structure has three thousand base pairs, compared to the three billion base pairs in human genomes. A base pair consists of the 4 nucleotides called A, C, G, T   which comprise one rung of the DNA ladder. So a successful gene edit would have to identify the precise rung of the DNA ladder where the mutation had occurred which means at least one of the 4 letters of the base pair was incorrect and correct it.

So I theorize that a life progenitor would have to be something that is ubiquitous in the universe and capable of starting life with a minimal genome which consists of only a few base pairs. This is a mystery but certainly not the only one. Gravity is an every day phenomenon but no one has detected a graviton which is thought to be the physical entity that distorts space time according to Einstein's theory of relativity. No one understands the "dark energy" which is thought to be responsible for the fact that the universe is not only expanding but accelerating. No one understands what Einstein called "spooky action at a distance" which has been demonstrated to be a reality in quantum theory. Just as the line is blurred between what is material and what is massless energy, the line is blurred between what is spiritual and what is material. Is the creation of life in the universe a physical, material phenomenon or a spiritual one?

Experts Warn This Industry-Backed Attack on Science at EPA Would Be Among 'Most Damaging' of All Trump-Era Policies

Published on Tuesday, November 12, 2019

by Common Dreams

"Let's call this what it is: an excuse to abandon clean air, clean water, and chemical safety rules."

by Jessica Corbett, staff writer

 

11 Comments

A stop sign stands outside the Environmental Protection Agency building on May 24, 2013 in Washington, D.C. (Photo: Mark Wilson/Getty Images)

Advocates of strong public health protections responded with alarm to a Monday night New York Times report on the Environmental Protection Agency's new draft proposal for the Trump administration's drawn-out effort to dramatically scale back the scientific research that can be used in government policymaking.

"Let's call this what it is: an excuse to abandon clean air, clean water, and chemical safety rules," said Andrew Rosenberg, director of the Center for Science and Democracy at the Union of Concerned Scientists. "This is a blatant removal of well-established science from the policymaking process, to the benefit of polluters and at a huge cost to the marginalized communities who face the biggest threat from pollution."

Trump Administration is making it easier to pollute our air and water for the profit of corporations. This literally does not make us great again. It makes us sick.

E.P.A. to Tighten Limits on Science Used to Write Public Health Rules https://t.co/d9oYS0vCh1

— Wajahat Ali (@WajahatAli) November 11, 2019

The draft proposal (pdf), titled "Strengthening Transparency in Regulatory Science," would force the agency to only consider research that discloses all raw data, including private medical files. It follows a similar proposal unveiled by former EPA chief Scott Pruitt in April 2018 that provoked nearly 600,000 comments from the public, the majority of which were critical.

Pruitt's successor as EPA administrator, ex-lobbyist Andrew Wheeler, delayed the prior proposal, purportedly to consider concerns from environmental and public health groups. However, the new version "headed for White House review and obtained by The New York Times shows that the administration intends to widen its scope, not narrow it."

According to the Times:

The measure would make it more difficult to enact new clean air and water rules because many studies detailing the links between pollution and disease rely on personal health information gathered under confidentiality agreements. And, unlike a version of the proposal that surfaced in early 2018, this one could apply retroactively to public health regulations already in place.

"This means the EPA can justify rolling back rules or failing to update rules based on the best information to protect public health and the environment, which means more dirty air and more premature deaths," said Paul Billings, senior vice president for advocacy at the American Lung Association.

Public health experts warned that studies that have been used for decades—to show, for example, that mercury from power plants impairs brain development, or that lead in paint dust is tied to behavioral disorders in children—might be inadmissible when existing regulations come up for renewal.

One key example of scientific research that wouldn't be permissible for government use under the EPA proposal is a 1993 Harvard University project known as the Six Cities study, which connected air pollution to premature deaths and subsequently informed nationwide air quality policies.

"A separate internal EPA memo viewed by The New York Times shows that the agency had considered, but ultimately rejected, an option that might have allowed foundational studies like Harvard's Six Cities study to continue to be used," the newspaper reported Monday.

As journalist Emily Atkin put it in her HEATED newsletter Tuesday: "In other words, air pollution denial is becoming U.S. policy for the first time." She noted that this proposal "is a key priority of Steve Milloy, a former tobacco and fossil fuel industry lobbyist who served on Trump's EPA transition team."

Atkin recalled speaking with Stan Glantz, a professor of tobacco control at the University of California San Francisco, when reporting on Pruitt's version of the proposal last year. The tobacco industry, Glantz told her, "realized that, rather than fighting every single study that came out linking them to cancer, if they could get the rules of evidence changed, they wouldn't have to worry about it."

The Times report on Wheeler's revived and expanded version elicited impassioned warnings and critiques on Twitter:

If somebody had a long-term plan to return us to the Dark Ages, this would be one of the steps. https://t.co/BQRA0Ftixo

— Kurt Andersen (@KBAndersen) November 12, 2019

A dangerous move that will impact the health of our communities today & for decades to come. Also attacking rigorous scientific research; data on vulnerable populations must be protected to assure the best science and true public health protections https://t.co/cncrXXQBBA

— Carmen Marsit (@CMarsit) November 12, 2019

The safety of the air we breath and water we drink shouldn’t be partisan. But sadly is, as R lawmakers in the pocket of industry work to unwind significant protections. Care about the health and safety of your kids? Vote them out. #TX21 https://t.co/cgHjVOksoK via @NYTimes

— Wendy Davis (@wendydavis) November 12, 2019

An EPA spokesperson told the Times in an emailed statement that "the agency does not discuss draft, deliberative documents, or actions still under internal and interagency review." Wheeler, for his part, said in September that "we're moving forward [with the proposal] to ensure that the science supporting agency decisions is transparent and available for evaluation by the public and stakeholders."

UCS's Rosenberg said Tuesday that "Wheeler's claims about the need for these restrictions don't pass the laugh test. Everything about this rule makes a mockery of the EPA's claim that this change is necessary for transparency. This rule was driven by political operatives. It's being rushed through with minimal opportunity for public comment. And it introduces pointless hurdles and delays into the policymaking process that will compromise the federal government's ability to protect the public."

"The Trump administration has a clear pattern of sidelining science and undermining public health protections," he added. "If this rule is finalized, it would be one of the most damaging and far-reaching policy changes enacted by the administration. It would put the entire enterprise of developing science-based public health safeguards at risk."

The Times report came ahead of a Wednesday morning hearing planned by the Democrat-controlled U.S. House Science, Space, and Technology Committee about the Trump administration's effort to restrict the use of scientific research in federal policymaking, which will feature testimony from various scientists and public health experts.

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Off the Top of My Head

Blackholes and Shitholes

by John Lawrence

There is an excellent  two hour show on Nova about black holes. It seems they are ubiquitous in the universe. They seem to be at the center of every galaxy and elsewhere in the galaxies as well. Whereas light escapes from the stars and makes it's way to the earth where astronomers can study them, light cannot escape from a black hole simply because it is so massive that its gravity won't let it. This seems easy enough to understand. Light has mass as Einstein demonstrated so it's subject to being attracted by gravity just as Newton's apple was. A star might be called a light hole because its mass is not great enough to suck photons back to it so they escape. A black hole could be thought of as a massive star with the characteristic that light cannot escape. So what's the big deal?

There are a whole host of interesting objects in the universe for astronomers to study and get excited about. That's fine. They just recently in 2017 measured a gravity wave. It took two massive installations that must have cost millions of dollars to do it. Whether any practical applications can come out of gravity waves, which were created by two black holes colliding, remains to be seen. Anyway three scientists won a Nobel prize because of the discovery. It's interesting that somewhere else in the universe billions of years ago the two black holes which produced the gravity wave collided. And just last year the gravity wave traveling at the speed of light washed over the earth. If the scientist at one of the LIGO installations hadn't gone home at 4 AM and taken the installation out of test mode, they never would have seen it.

Scientists don't understand about the dark matter and energy that evidently exists in the universe. The dark matter could simply by the sum total of the masses of black holes. I don't see why they don't explain it that way. As for dark energy, well it goes to show that scientists just do not understand everything about the universe. There's still a lot to discover. It also seems that every little discovery requires massive, million dollar installations. Remember the super conducting super collider which cost millions? It finally was able to detect the last "God" particle, the Higgs boson!

Well, measuring gravity waves produced by the collision of two black holes is nice, couldn't all the money that went into it have been better spent eradicating disease and poverty in parts of the world that Trump calls "shitholes"? The energy and efforts of talented individuals could better be spent eliminating war and suffering around the world, not to mention homelessness in America. We don't need technological innovation so much as we need to solve problems here on earth that human societies have been grappling with for millenia.

Off the Top of My Head

We Have Been Given a Great Gift: Our Individual Identities

by John Lawrence

Whether or not we were created by God, the universe, evolution or the Great Whatever, we got here somehow. It's not clear exactly how but in any case we have been given an individual identity and we have free will. We can pretty much, within certain constraints, decide what we are going to do today. This gift may be time limited in that it might end at some point in time just as it had a beginning at some point in time. It doesn't make it any less of a gift if it does end, if it doesn't continue in some other time and space after we die.

If someone gives you a gift, say $10,000, you don't complain that they didn't give you a bigger gift. The gift was limited in its monetary value but it still was a gift to be thankful for. By the same token if the gift of individual identity doesn't continue after we die, it is still a tremendous gift to be grateful for. Life still goes on with other life forms including people and perhaps in other places in the universe. And whether this gift was given to us by God or the Great Whatever, it is still a gift to be thankful for.

The Equivalence Principle plays a big part in science. In the theory of general relativity, the Equivalence Principle as developed by Albert Einstein was that the gravitational force as experienced locally while standing on the Earth is the same as the pseudo-force experienced by an observer in an accelerated frame of reference. I think that the Equivalence Principle as applied to life is that whatever happens to any lifeform after death is the same for all lifeforms.

So if I swat a fly on the wall, thereby causing its life to come to a sudden end, whatever then happens to that fly is the same thing that will happen to me or any other life form after its life ends. But I don't really believe there is a fly afterlife or a fly heaven. I believe individual lives are time limited. It makes that life no less a gift to be thankful for. Rather than saying, but you should have given me more, say gee that was great and thanks for that even if at some point it's over. Same applies to a gift of money or a relationship for that matter.

Even if our individual identity ends, it was still a great gift while it lasted.

Open Science And The Econoblogosphere

by Paul Krugman

from the New York Times, January 17, 2012

Interesting article in the Times about the push for “open science”, bypassing the traditional structure of refereed journals in favor of a sort of fluid, self-policing online community. I can’t and won’t weigh in on this issue with regards to hard science, but I think there are some interesting parallels with what has been happening in economics.

This is also, by the way, a chance for me to maunder on about what it was like when I was younger. You kids get off my lawn!

So, the starting point for me, when thinking about how economics works as a discipline, is to realize that the traditional model of submit, get refereed, publish, and then people will read your work broke down a long time ago. In fact, it had more or less fallen apart by the early 80s.Even then, nobody at a top school learned stuff by reading the journals; it was all working papers, with the journals serving as tombstones.

And how did you know which working papers to read? In the fields I worked in, NBER Working Papers — yellowjackets — became the principal outlet for new research. If you were an associate, you got those papers in the mail, and at least checked out the abstracts — and if you were in the loop, you got to put out your own work the same way.

And who was in the loop? Well, there were groups of people in each subfield that were the real centers of information and reputation. I was part of two such groups, one in real trade, one in international money. I referred at the time to the “floating crap game”, hence the video above — there would be various conferences around the world, but the same 30 or so people would show up at each conference, like Nathan Detroit’s gamblers finding different hideouts each night.

You got provisional entree to such a group through connections — basically, being a student of someone who mattered, and being tagged as having potential. You got permanent membership by doing enough clever stuff; the informal rule was three good papers, one to get noticed, one to show that the first wasn’t a fluke, one to show that you had staying power.

And journal publication? Well, tenure committees needed that, but it was so slow relative to the pace of ongoing work that it no longer acted as an information conduit. I presented my paper on target zones at a 1988 conference; by the time it was formally published, in 1991, I had to add a section on the subsequent literature, because there were around 150 derivative papers already out there.

The whole thing was informal — and also deeply undemocratic, offering very little way for outsiders to enter the debate.

So now we have rapid-fire exchange via blogs and online working papers — and I think it’s all good. Work circulates even faster than it did then, there are quick exchanges that can advance understanding, and while it’s still hard to break in, connections aren’t as important as they once were and the system is much more open.

But, you say, doesn’t this allow a lot of really bad economics to circulate? Yes, but is it really any worse than it used to be? As I’ve tried to explain, the notion of journals as gatekeepers was largely fictional even 25 years ago. And I have a somewhat jaundiced view of how the whole refereeing/publication system has ever worked; all too often, it seems to act as a way for entrenched doctrines to blockade new ideas, or at least to keep people with new ideas from getting tenure at a good school.

The major problem I see now is the disconnect between promotion and the real nature of intellectual discourse in the Internet age. But the quality of the discussion, it seems to me, is if anything higher than it was in the good old days.

Evolution and Creationism Not Incompatible?

Evolution Presupposes Design, So Why the Controversy?

by Ervin Laszlo

Systems philosopher, integral theorist, concert pianist

Posted: April 15, 2010 04:17 PM

The debate among conservative Christians, Muslims, and Jews (the "creationists") and natural scientists and the science-minded public (the "evolutionists") centers on biological evolution. But on a deeper level, it concerns the universe in which life has evolved -- or in which it was created. And, as I will argue, on this level there is no contradiction between design and evolution: both are equally needed to explain the facts.

At first glance, the scientific community -- and anyone who believes that science can tell us something about the nature of reality -- is compelled to reject the hypothesis that all organisms are the way they are because they were designed to be that way. But the creationists question that the stupendously varied panoply of life arose from mutations in the genome occurring by chance with the resulting organisms fitting by chance into environments where they can reproduce better than their predecessors. Such a chance-mutation and lucky-environmental-fit process is surely too "hit or miss" to have created the complex web of life in the biosphere. The theory that affirms it is bound to be false.

However, at the cutting edge of science, the theory of evolution doesn't rely on random serendipity. That view marks the classical Darwinist position, still championed by a few (though always fewer) mainline biologists. Richard Dawkins, for example, insists that the living world is the result of processes of piecemeal trial and error, without deeper meaning and significance. Evolution happens, but there is no purpose and meaning to it.

Take cheetahs, said Dawkins. They give every indication of being superbly designed to kill antelopes. The teeth, claws, eyes, nose, leg muscles, backbone, and brain of a cheetah are all precisely what we should expect if God's purpose in creating cheetahs was to maximize deaths among antelopes. At the same time, antelopes are fast, agile, and watchful, apparently designed so they can escape cheetahs. Yet neither the one feature nor the other implies creation by design: this is just the way nature is. Cheetahs have a "utility function" to kill antelopes, and antelopes have a utility function to escape cheetahs. Nature itself is indifferent to this game. This is a world of blind physical forces and genetic replication where some get hurt and others flourish. It has precisely the properties we would expect it to have if there were no design, no purpose, and no evil and no good in the world, only blind indifference.

If a Designer is responsible for the way the living world works, He/She would have to be at best indifferent to what comes about in that world, or at worst a sadist who enjoys blood sports. It's more reasonable, according to Dawkins, to hold that the world just is, without reason and purpose. The way it is results from random processes played out within limits set by fundamental physical laws. The idea of design is superfluous. Classical Darwinists echo French mathematician Pierre Laplace, who is reputed to have said to Napoleon that God is a hypothesis for which there is no longer any need.

Confronted with the classical theory, creationists are justified in pointing out that it's extremely improbable that all we see in the world of life, ourselves included, should be the result of chance processes governed by impersonal laws. The idea that everything evolved by blind chance out of common and simple origins is just theory, they say. The world is more than a random assembly of disjointed elements; it exhibits meaning and purpose. This implies design.

The creationist position would be the logical choice if -- but only if -- scientists would persist in claiming that the evolution of living species is a product of two-fold serendipity. But at the cutting edge, scientists no longer claim this. Post-Darwinian biologists recognize that the evolution of species is far more than the chance processes classical Darwinists say it is. It must be more, because the time that was available for evolution would not have been sufficient to generate the complex web of life on this planet merely by trial and error. Mathematical physicist Sir Fred Hoyle calculated the probabilities and came to the conclusion that they are about the same as the probability that a hurricane blowing through a scrap-yard assembles a working airplane.

Leading-edge scientists realize that the evolution of organic species is an orderly, highly coordinated process, even if it's not mechanistic and deterministic. The evolution of the living world is part of the great wave that created particles from the underlying virtual-energy and information field misleadingly called "vacuum" (and is better called unified field, nuether, or Akashic field). The wave unfolded in the cosmos by structuring particles into atoms, atoms into molecules, molecules into macromolecules and cells, cells into organisms, and organisms and populations of organisms into local, regional, and continental ecologies.

The wave of evolution could only have unfolded in a universe where the fundamental laws and constants are finely tuned to permit the emergence of complexity. Ours is such a universe. Physicists know that even a minute difference in these laws and constants would have foreclosed the possibility of life forever.

Our universe is staggeringly fine-tuned to the creation of systems of higher and higher orders of complexity, differentiation, and integration. That such a universe would have come about by chance is astronomically improbable. According to quantum cosmology, some 1 x 10⁵⁰⁰ (1 followed by five hundred zeros) universes could exist physically, but only a handful could give rise to life. That our life-supporting universe would have come about by a random selection from this enormous set of possible universes is a zillion times more improbable than that living species would have come about by random mutations. The great wave of evolution requires highly harmonized and coordinated processes in all its domains.

In the final count the evolution of life presupposes intelligent design. But the design it presupposes is not the design of the products of evolution; it's the design of its preconditions. Given the right preconditions, nature comes up with the products on her own.

The debate between creationists and evolutionists would be better focused on the origins of the universe than on the origins of life. Could it be that our universe has been purposefully designed so it could give rise to the evolution of life? For creationists, this would be the logical assumption. Evolutionists could not object: evolution, being an irreversible process, must have had a beginning, and that beginning must be accounted for. And our fine-tuned universe is entirely unlikely to have come about by chance.

So the creationist/evolutionist controversy really is pointless. Design is a necessary assumption, because chance doesn't explain the facts. But evolution is likewise a necessary assumption, for given the way this universe works, the evolution of complexity is a logical and by now well-documented consequence. Therefore the rational conclusion is not design or evolution. It's design for evolution.

Then why the controversy?