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CT scans may account for 5% of all cancers annually, according to a new study that cautions against overusing and overdosing CTs. The danger is greatest for infants, followed by children and adolescents. But adults also are at risk, since they are the most likely to get scans.

Deep sea mining operations are expected to increase the negative impact on environmental indicators by up to 13 per cent, a change categorized as having 'great' significance, relative to the 'without' DSM scenario, notably through increased coastal vulnerability, pollution, and biodiversity loss.

MXenes are materials with almost miraculous properties: they can be used for electromagnetic shielding, for energy storage or for novel sensors. It was recently found that they are also amazingly suitable as solid lubricants, even under the harshest conditions, for example in space technology. The only problem so far has been that producing these MXenes was considered extremely dangerous and toxic. But now a new method has been developed: instead of a toxic acid, electricity is used.

Using smartphones, computers and the internet seems to slow cognitive decline in people aged over 50

We’ve now figured out how to culture chocolate in the lab. The breakthrough could help with spiralling cocoa costs, and may even lead to tastier treats with more nutritional value

An antibiotic that is commonly used for urinary tract infections effectively treated gonorrhoea, and may even work against drug-resistant cases

I revised my will about three weeks ago, as I realized that two of my impecunious friends to whom I was leaving money were dead. (Don’t worry–I’m fine!) Plus some of the charities to which I’d pledged money were no longer appealing to me (that means you, Doctors Without Borders), so I found a passel of other charities, vetted by Peter Singer’s “The Life You Can Save” site and Charity Navigator, to replace them. I won’t go into details save to say that what I leave will go in general to four causes:  helping the poor in third-world countries, especially with sanitation and medical care for children, ensuring education for women in poor countries, conservation effected through buying up habitat for wildlife and plants, and conservation effected by helping animals (this does of course include big cats!).

When I made my list and handed it to the lawyer, I discovered I still had a chunk o’ cash left, and pondered what I should do with it.  I’ve lived pretty penuriously and don’t have any luxuries, and the last thing I’d need would be something pricey like a luxury car. My only indulgences are travel and wine.

And then I had an idea: create a graduate fellowship for Ph.D. students who need research money in evolutionary biology. If I started that while I was still alive, I could actually see the results as they played out in real time: research would be done and truth found.  Then I had an even better idea: if the fellowship were named after me, I could add the name of my favorite mallard: Honey the Duck.  After checking with the University, I found out that I not only had enough to endow a decent fellowship in perpetuity, but also they would also allow me to add Honey’s name!

And that is how the Jerry Coyne/Honey the Duck Evolutionary Biology Research Fund came to be. To wit (this is part of a three-page agreement). Click to enlarge:

For Chicago grad students who would like to tap into this dosh, I’ll say a few words. The money will increase over time from $5000 the first year to around $25,000 per year in perpetuity after 2030.  I intend it to go, as the note says above, for research expenses in evolutionary biology studies that involve whole organisms. This reflects my own interests when I was active and is aimed at keeping organismal evolutionary biology (which can of course also involve behavior, molecular work, and so on) alive in the department.  But whole organisms have to be involved in some way. These details may be refined when I make up the application for the money, as it’s a competitive process.

More than one student may be funded per year, and once the money is allotted, it will be there until the student gets their Ph.D. Leftover cash will be returned to the fund.  Only students who have passed their prelims, and are thus official candidates for the doctorate, can apply, and I hope the first applications will be handed out in the early fall.

One other thing: once the money is in the hands of the Division (only students in the Division of Biological Science [BSD] can apply), my role ends, as it should. I will have no hand in choosing students who get funded: that will be done by a committee appointed by our chairman. That’s appropriate because the field changes over time and I am retired.

I’m giving these details just so students know that next fall there will be a new pot of money to fund research. I also love the fact that I can name the fund after both myself and Honey the Duck: faithful companions for several years. There is too little humor in science, and I wonder if this is the first graduate fellowship in history to be named after a duck.

Here are two pictures: my favorite one of Honey, and the second of me feeding Honey by hand during the pandemic (I was outside and the campus was empty, ergo the pulled-down mask).  I will try to put these photos on the application. Evolutionary biology students in the BSD should watch for an announcement by the Higher Ups.

One of the best parts of it all is that Honey and I will be immortalized together–or at least linked together until there is no more evolutionary biology at the University of Chicago.

Quack!

Honey as a soccer ball

 

Me with my favorite hen of all time

Addendum: from reader Bill with the help of Grok 3

Unfortunately, the press of work yesterday made me completely forget it was Sunday, and the day to post John Avise‘s latest and last group of North American butterfly photos. John’s captions and IDs are indented, and you can enlarge the photos by clicking on them.  Let’s hear it for John’s butterfly photos? Will a new species replace them? You’ll have to wait and see.

Butterflies in North America, Part 18

This week concludes my multi-part series on North American butterflies.With this post, we’ve finally reached the letter Z (of common names), so this will be my final post on the many butterfly species found on this continent.

Western Pygmy Blue (Brephidium exilis), male:

Western Pygmy Blue, female:

Western Pygmy Blue, underwing

Western Tiger Swallowtail (Papilio rutulus), upperwing:

Western Tiger Swallowtail, underwing:

Eurasian White Admiral (Limenitis camilla):

White Checkered-skipper (Burnsius albescens):

Woodland Skipper (Ochlodes sylvanoides), upperwing:

Woodland Skipper, underwing:

Wright’s Metalmark (Calephelis wrighti), upperwing:

Wright’s Metalmark, underwing:

Zebra Longwing (Heliconius charithonia), upperwing:

Zebra Longwing, underwing:

We’ll get back to measurement, interference and the double-slit experiment just as soon as I can get my math program to produce pictures of the relevant wave functions reliably. I owe you some further discussion of why measurement (and even interactions without measurement) can partially or completely eliminate quantum interference.

But in the meantime, I’ve gotten some questions and some criticism for arguing that superposition is an OR, not an AND. It is time to look closely at this choice, and understand both its strengths and its limitations, and how we have to move beyond it to fully appreciate quantum physics. [I probably should have written this article earlier — and I suspect I’ll need to write it again someday, as it’s a tricky subject.]

The Question of Superposition

Just to remind you of my definitions (we’ll see examples in a moment): objects that interact with one another form a system, and a system is at any time in a certain quantum state, consisting of one or more possibilities combined in some way and described by what is often called a “wave function”. If the number of possibilities described by the wave function is more than one, then physicists say that the state of the quantum system is a superposition of two or more basic states. [Caution: as we’ll explore in later posts, the number of states in the superposition can depend on one’s choice of “basis”.]

As an example, suppose we have two boxes, L and R for left and right, and two atoms, one of hydrogen H and one of nitrogen N. Our physical system consists of the two atoms, and depending on which box each atom is in, the system can exist in four obvious possibilities, shown in Fig. 1:

• HL NL (i.e. both the hydrogen atom and the nitrogen atom are in the left box)
• HL NR
• HR NL
• HR NR

Figure 1: The four intuitively obvious options for how to store the two atoms in the boxes correspond to four basic states of the quantum system.

Before quantum physics, we would have thought those were the only options; each atom must be in one box or the other. But in quantum physics there are many more non-obvious possibilities.

In particular, we could put the system in a superposition of the form HL NL + HR NR, shown in Fig. 2. In the jargon of physics, “the system is in a superposition of HL NL and HR NR“. Note the use of the word “and” here. But don’t read too much into it; jargon often involves linguistic shorthand, and can be arbitrary and imprecise. The question I’m focused on here is not “what do physicists say?”, but “what does it actually mean?”

Figure 2: A quantum system can be in a superposition, such as this one represented by two basic states related by a “+” symbol. (This is not the most general case, as discussed below.)

In particular, does it mean that “HL NL AND HR NR” are true? Or does it mean “HL NL OR HR NR” is true? Or does it mean something else?

The Problems with “AND”

First, let’s see why the “AND” option has a serious problem.

In ordinary language, if I say that “A AND B are true”, then I mean that one can check that A is true and also, separately, that B is true — i.e., both A and B are true. With this meaning in mind, it’s clear that experiments do not encourage us to view superposition as an AND. (There are theory interpretations of quantum physics that do encourage the use of “AND”, a point I’ll return to.)

Experiment Is Skeptical

Specifically, if a system is in a quantum superposition of two states A and B, no experiment will ever show that

• A is true
  AND
• B is true.

Instead, in any experiment explicitly designed to check whether A is true and whether B is true, the result will only reveal, at best, that

• A is true and B is not true
  OR
• B is true and A is not true.

The result might also be ambiguous, neither confirming nor denying that either one is true. But no measurement will ever show that both A AND B are definitively true. The two possibilities A and B are mutually exclusive in any actual measurement that is sensitive to the question.

In our case, if we go looking for our two atoms in the state HL NL + HR NR — if we do position measurements on both of them — we will either find both of them in the left box OR both of them in the right box. 1920’s quantum physics may be weird, but it does not allow measurements of an atom to find it in two places at the same time: an atom has a position, even if it is inherently uncertain, and if I make a serious attempt to locate it, I will find only one answer (within the precision of the measurement). [Measurement itself requires a long discussion, which I won’t attempt here; but see this post and the following one.]

And so, in this case, a measurement will find that one box has two atoms and the other has zero. Yet if we use “AND” in describing the superposition, we end up saying “both atoms are in the left box AND both atoms are in the right box”, which seems to imply that both atoms are in both boxes, contrary to any experiment. Again, certain theoretical approaches might argue that they are in both boxes, but we should obviously be very cautious when experiment disagrees with theoretical reasoning.

The Fortunate and/or Unfortunate Cat

The example of Schrodinger’s cat is another context in which some writers use “and” in describing what is going on.

A reminder of the cat experiment: We have an atom which may decay now or later, according to a quantum process whose timing we cannot predict. If the atom decays, it initiates a chain reaction which kills the cat. If the atom and the cat are placed inside a sealed box, isolating them completely from the rest of the universe, then the initial state, with an intact atom (Ai) and a Live cat (CL), will evolve to a state in a superposition roughly of the form Ai CL + Ad CD, where Ai refers to a decayed atom and CD refers to a Dead cat. (More precisely, the state will take the form c1 Ai CL + c2 Ad CD, where c1 and c2 are complex numbers with |c1|2 + |c2|2 = 1; but we can ignore these numbers for now.)

Figure 3: As in Figure 2, a superposition can even, in principle, be applied to macroscopic objects. This includes the famous Schrodinger cat state.

Leaving aside that the experiment is both unethical and impossible in practice, it raises an important point about the word “AND”. It includes a place where we must say “AND“; there’s no choice.

As we close the box to start the experiment, the atom is intact AND the cat is alive; both are simultaneously true, as measurement can verify. The state that we use to describe this, Ai CL, is a mathematical product: implicitly “Ai CL” means Ai x CL, where x is the “times” symbol.

Figure 4: It is unambiguous that the initial state of the cat-atom system is that the atom is intact AND the cat is alive: Ai x CL.

Later, the state to which the system evolves is a sum of two products — a superposition (Ai x CL) + (Ad x CD) which includes two “AND” relationships

1) “the atom is intact AND the cat is alive” (Ai x CL)
2) “the atom has decayed AND the cat is dead” (Ad x CD)

In each of these two possibilities, the state of the atom and the state of the cat are perfectly correlated; if you know one, you know the other. To use language consistent with English (and all other languages with which I am familiar), we must use “AND” to describe this correlation. (Note: in this particular example, correlation does in fact imply causation — but that’s not a requirement here. Correlation is enough.)

It is then often said that, theoretically, that “before we open the box, the cat is both alive AND dead”. But again, if we open the box to find out, experimentally, we will find out either that “the cat is alive OR the cat is dead.” So we should think this through carefully.

We’ve established that “x” must mean “AND“, as in Fig. 4. So let’s try to understand the “+” that appears in the superposition (Ai x CL) + (Ad x CD). It is certainly the case that such a state doesn’t tell us whether CL is true or CD is true, or even that it is meaningful to say that only one is true.

But suppose we decide that “+” means “AND“, also. Then we end up saying

• “(the cat is alive AND the atom is intact) AND (the cat is dead AND the atom has decayed.)”

That’s very worrying. In ordinary English, if I’m referring to some possible facts A,B,C, and D, and I tell you that “(A AND B are true) AND (C AND D are true)”, the logic of the language implies that A AND B AND C AND D are all true. But that standard logic would leads to a falsehood. It is absolutely not the case, in the state (Ai x CL) + (Ad x CD), that CL is true and Ad is true — we will never find, in any experiment, that the cat is alive and yet the atom has decayed. That could only happen if the system were in a superposition that includes the possibility Ad x CL. Nor (unless we wait a few years and the cat dies of old age) can it be the case that CD is true and Ai is true.

And so, if “x” means “AND” and “+” means “AND“, it’s clear that these are two different meanings of “AND.”

“AND” and “AND”

Is that okay? Well, lots of words have multiple meanings. Still, we’re not used to the idea of “AND” being ambiguous in English. Nor are “x” and “+” usually described with the same word. So using “AND” is definitely problematic.

(That said, people who like to think in terms of parallel “universes” or “branches” in which all possibilities happen [the many-worlds interpretation] may actually prefer to have two meanings of “AND”, one for things that happen in two different branches, and one for things that happen in the same branch. But this has some additional problems too, as we’ll see later when we get to the subtleties of “OR”.)

These issues are why, in my personal view, “OR” is better when one first learns quantum physics. I think it makes it easier to explain how quantum physics is both related to standard probabilities and yet goes beyond it. For one thing, “or” is already ambiguous in English, so we’re used to the idea that it might have multiple meanings. For another, we definitely need “+” to be conceptually different from “x“, so it is confusing, pedagogically, to start right off by saying that both mathematical operators are “AND”.

But “OR” is not without its problems.

The Problems with “OR”

In normal English, saying “the atom is intact and the cat is alive” OR “the atom has decayed and the cat is dead” would tell us two possible facts about the current contents of the box, one of which is definitely true.

But in quantum physics, the use of “OR” in the Schrodinger cat superposition does not tell us what is currently happening inside the box. It does tell us the state of the system at the moment, but all that does is predict the possible outcomes that would be observed if the box were opened right now (and their probabilities.) That’s less information than telling us the properties of what is in the closed box.

The advantage of “OR” is that it does tell us the two outcomes of opening the box, upon which we will find

• “The atom is intact AND the cat is alive”
  OR
• “The atom has decayed AND the cat is dead”

Similarly, for our box of atoms, it tells us that if we attempt to locate the atoms, we will find that

• “the hydrogen atom is in the left box AND the nitrogen atom is in the left box”
  OR
• “the hydrogen atom is in the right box AND the nitrogen atom is in the right box”

In other words, this use of AND and OR agrees with what experiments actually find. Better this than the alternative, it seems to me.

Nevertheless, just because it is better doesn’t mean it is unproblematic.

The Usual Or

The word “OR” is already ambiguous in usual English, in that it could mean

• either A is true or B is true
• A is true or B is true or both are true

Which of these two meanings is intended in an English sentence has to be determined by context, or explained by the speaker. Here I’m focused on the first meaning.

Returning to our first example of Figs. 1 and 2, suppose I hand the two atoms to you and ask you to put them in either box, whichever one you choose. You do so, but you don’t tell me what your choice was, and you head off on a long vacation.

While I wait for you to return, what can I say about the two atoms? Assuming you followed my instructions, I would say that

• “both atoms are in the left box OR both atoms are in the right box”

In doing so, I’m using “or” in its “either…or…” sense in ordinary English. I don’t know which box you chose, but I still know (Fig. 5) that the system is either definitely in the HL NL state OR definitely in the HR NR state of Fig. 1. I know this without doing any measurement, and I’m only uncertain about which is which because I’m missing information that you could have provided me. The information is knowable; I just don’t have it.

Figure 5: The atoms were definitely put into in one box or the other, but nobody told me which box was selected.

But this uncertainty about which box the atoms are in is completely different from the uncertainty that arises from putting the atoms in the superposition state HL NL + HR NR!

The Superposition OR

If the system is in the state HL NL + HR NR, i.e. what I’ve been calling (“HL NL OR HR NR“), it is in a state of inherent uncertainty of whether the two atoms are in the left box or in the right box. It is not that I happen not to know which box the atoms are in, but rather that this information is not knowable within the rules of quantum physics. Even if you yourself put the atoms into this superposition, you don’t know which box they’re in any more than I do.

The only thing we can try to do is perform an experiment and see what the answer is. The problem is that we cannot necessarily infer, if we find both atoms in the left box, that the two atoms were in that box prior to that measurement.

If we do try to make that assumption, we find ourselves in apparent contradiction with experiment. The issue is quantum interference. If we repeat the whole process, but instead of opening the boxes to see where the atoms are, we first bring the two boxes together and measure the atoms’ properties, we will observe quantum interference effects. As I have discussed in my recent series of five posts on interference (starting here), quantum interference can only occur when a system takes at least two paths to its current state; but if the two atoms were definitely in one box or definitely in the other, then there would be only one path in Fig. 6.

Figure 6: In the superposition state, the atoms cannot simply be in definite but unknown locations, as in Fig. 5. If the boxes are joined and then opened, quantum interference will occur, implying the system has evolved via two paths to a single state.

Prior to the measurement, the system had inherent uncertainty about the question, and while measurement removes the current uncertainty, it does not in general remove the past uncertainty. The act of measurement changes the state of the system — more precisely, it changes the state of the larger system that includes both atoms and the measurement device — and so establishing meaningfully that the two atoms are now in the left box is not sufficient to tell us meaningfully that the two atoms were previously and definitively in the left box.

So if this is “OR“, it is certainly not what it usually means in English!

This Superposition or That One?

And it gets worse, because we can take more complex examples. As I mentioned when discussing the poor cat, the superposition HL NL + HR NR is actually one in a large class of superpositions, of the form c1 HL NL + c2 HR NR , where c1 and c2 are complex numbers. A second simple example of such a superposition is HL NL – HR NR, with a minus sign instead of a plus sign.

So suppose I had asked you to put the two atoms in a superposition either of the form HL NL + HR NR or HL NL – HR NR, your choice; and suppose you did so without telling me which superposition you chose. What would I then know?

I would know that the system is either in the state (HL NL + HR NR) or in the state (HL NL – HR NR), depending on what you chose to do. In words, what I would know is that the system is represented by

• (HL NL OR HR NR) OR (HL NL OR HR NR)

Uh oh. Now we’re as badly off as we were with “AND“.

First, the “OR” in the center is a standard English “OR” — it means that the system is definitely in one superposition or the other, but I don’t know which one — which isn’t the same thing as the “OR“s in the parentheses, which are “OR“s of superposition that only tell us what the results of measurements might be.

Second, the two “OR“s in the parentheses are different, since one means “+” and the other means “–“. In some other superposition state, the OR might mean 3/5 + i 4/5, where i is the standard imaginary number equal to the square root of -1. In English, there’s obviously no room for all this complexity. [Note that I’d have the same problem if I used “AND” for superpositions instead.]

So even if “OR” is better, it’s still not up to the task. Superposition forces us to choose whether to have multiple meanings of “AND” or multiple meanings of “OR”, including meanings that don’t hold in ordinary language. In a sense, the “+” (or “-” or whatever) in a superposition is a bit more “AND” than standard English “OR”, but it’s also a bit more “OR” than a standard English “AND”. It’s something truly new and unfamiliar.

Experts in the foundational meaning of quantum physics argue over whether to use “OR” or “AND”. It’s not an argument I want to get into. My goal here is to help you understand how quantum physics works with the minimum of interpretation and the minimum of mathematics. This requires precise language, of course. But here we find we cannot avoid a small amount of math — that of simple numbers, sometimes even complex numbers — because ordinary language simply can’t capture the logic of what quantum physics can do.

I will continue, for consistency, to use “OR” for a superposition, but going forward we must admit and recognize its limitations, and become more sophisticated about what it does and doesn’t mean. One should understand my use of “OR“, and the “pre-quantum viewpoint” that I often employ, as pedagogical methodology, not a statement about nature. Specifically, I have been trying to clarify the crucial idea of the space of possibilities, and to show examples of how quantum physics goes beyond pre-quantum physics. I find the “pre-quantum viewpoint”, where it is absolutely required that we use “OR”, helps students get the basics straight. But it is true that the pre-quantum viewpoint obscures some of the full richness and complexity of quantum phenomena, much of which arises precisely because the quantum “OR” is not the standard “OR” [and similarly if you prefer “AND” instead.] So we have to start leaving it behind.

There are many more layers of subtlety yet to be uncovered [for instance, what if my system is in a state (A OR B), but I make a measurement that can’t directly tell me whether A is true or B is true?] but this is enough for today.

I’m grateful to Jacob Barandes for a discussion about some of these issues.

Conceptual Summary

• When we use “A AND B” in ordinary language, we mean “A is true and B is true”.
• When we use “A OR B” in ordinary language, we find “OR” is ambiguous even in English; it may mean
  • “either A is true or B is true”, or
  • “A is true or B is true or both are true.”
• In my recent posts, when I say a superposition c1 A + c2 B can be expressed as “A OR B”, I mean something that I cannot mean in English, because such a meaning would never normally occur to us:
  • I mean that the result of an appropriate measurement carried out at this moment will give the result A or the result B (but not both).
  • I do so without generally implying that the state of the system, if I don’t carry out the measurement, is definitely A or definitely B (though unknown).
  • Instead the system could be viewed as being in an uncanny state of being that we’re not used to, for which neither ordinary “AND” nor ordinary “OR” applies.
• Note also that using either “AND” or “OR” is unable to capture the difference between superpositions that involve the same states but differ in the numbers c1, c2.

The third bullet point is open to different choices about “AND” and “OR“, and open to different interpretation about what superposition states imply about the systems that are in them. There are different consistent ways to combine the language and concepts, and the particular choice I’ve made is pragmatic, not dogmatic. For a single set of blog posts that tell a coherent story, I have to to pick a single consistent language; but it’s a choice. Once one’s understanding of quantum physics is strong, it’s both valuable and straightforward to consider other possible choices.

Scientists have used gene editing to produce artificial electrical synapses in mice, where they can be targeted to make the animals more sociable or reduce their risk of OCD-like symptoms

Last week I wrote about the de-extinction of the dire wolf by a company, Colossal Biosciences. What they did was pretty amazing – sequence ancient dire wolf DNA and use that as a template to make 20 changes to 14 genes in the gray wolf genome via CRISPR. They focused on the genetic changes they thought would have the biggest morphological effect, so that the resulting pups would look as much as possible like the dire wolves of old.

This achievement, however, is somewhat tainted by overhyping what was actually achieved, by the company and many media outlets. Although the pushback began immediately, and there is plenty of reporting about the fact that these are not exactly dire wolves (as I pointed out myself). I do think we should not fall into the pattern of focusing on the controversy and the negative and missing the fact that this is a genuinely amazing scientific accomplishment. It is easy to become blase about such things. Sometimes it’s hard to know in reporting what the optimal balance is between the positive and the negative, and as skeptics we definitely can tend toward the negative.

I feel the same way, for example, about artificial intelligence. Some of my skeptical colleagues have taken the approach that AI is mostly hype, and focusing on what the recent crop of AI apps are not (they are not sentient, they are not AGI), rather than what they are. In both cases I think it’s important to remember that science and pseudoscience are a continuum, and just because something is being overhyped does not mean it gets tossed in the pseudoscience bucket. That is just another form of bias. Sometimes that amounts to substituting cynicism for more nuanced skepticism.

Getting back to the “dire wolves”, how should we skeptically view the claims being made by Colossal Biosciences. First let me step back a bit and talk about de-extinction – bringing back species that have gone extinct from surviving DNA remnants. There are basically three approaches to achieve this. They all start with sequencing DNA from the extinct species. This is easier for recently extinct species, like the carrier pigeon, where we still have preserved biological samples. The more ancient the DNA, the harder it is to recover and sequence. Some research has estimated that the half life of DNA (in good preserving conditions) is 521 years. This leads to an estimate that all base pairs will be gone by 6.8 million years. This means – no non-avian dinosaur DNA. But there are controversial claims of recovered dino DNA. That’s a separate discussion, but for now lets focus on the non-controversial DNA, of thousands to at most a few million years old.

Species on the short list for de-extinction include the dire wolf (13,000 years ago), woolly mammoth (10,000 years ago), dodo (360 years), and the thylacine (90 years). The best way (not the most feasible way) to fully de-extinct a species is to completely sequence their DNA and then use that to make a full clone. No one would argue that a cloned woolly mammoth is not a woolly mammoth. There has been discussion of cloning the woolly mammoth and other species for decades, but the technology is very tricky. We would need a complete woolly mammoth genome – which we have. However, the DNA is degraded making cloning not possible with current technology. But this is one potential pathway. It is more feasible for the dodo and thylacine.

A second way is to make a hybrid – take the woolly mammoth genome and use it to fertilize the egg from a modern elephant. The result would be half woolly mammoth and half Asian or African elephant. You could theoretically repeat this procedure with the offspring, breeding back with woolly mammoth DNA, until you have a creature that is mostly woolly mammoth. This method requires an extant relative that is close enough to produce fertile young. This is also tricky technology, and we are not quite there yet.

The third way is the “dino-chicken” (or chickenosaurus) method, promoted initially (as far as I can tell, but I’m probably wrong) by Jack Horner. With this method you start with an extant species and then make specific changes to its genome to “reverse engineer” an ancestor or close relative species. There are actually various approaches under this umbrella, but all involve starting with an extant species and making genetic changes. There is the Jurassic Park approach, which takes large chunks of “dino DNA” and plugs them into an intact genome from a modern species (why they used frog DNA instead of bird DNA is not clear). There is also the dino-chicken approach, which simply tries to figure out the genetic changes that happened over evolutionary time to result in the morphological changes that turned, for example, a theropod dinosaur into a chicken. Then, reverse those changes. This is more like reverse engineering a dinosaur by understanding how genes result in morphology.

Then we have the dire wolf approach – use ancient DNA as a template to guide specific CRISPR changes to an extant genome. This is very close to the dino-chicken approach, but uses actual ancient DNA as a template. All of these approaches (perhaps the best way to collectively describe these methods is the genetic engineering approach) do not result in a clone of the extinct species. They result in a genetically engineered approximation of the extinct species. Once you get passed the hype, everyone acknowledges this is a fact.

The discussion that flows from the genetic engineering method is – how do we refer to the resulting organisms? We need some catchy shorthand that is scientifically accurate. The three wolves produced by Colossal Biosciences are not dire wolves. But they are not just gray wolves – they are wolves with dire wolf DNA resulting in dire wolf morphological features. They are engineered dire wolf “sims”, “synths”, “analogs”, “echos”, “isomorphs”? Hmmm… A genetically engineered dire wolf isomorph. I like it.

Also, my understanding is that the goal of using the genetic engineering method of de-extinction is not to make a few changes and then stop, but to keep going. By my quick calculation the dire wolf and the gray wolf differ by about 800-900 genes out of 19,000 total. Our best estimate is that dire wolves had 78 chromosomes, like all modern canids, including the gray wolf, so that helps. So far 14 of those genes have been altered from gray wolf to dire wolf (at least enough to function like a dire wolf). There is no reason why they can’t keep going, making more and more changes based upon dire wolf DNA. At some point the result will be more like a dire wolf than a gray wolf. It will still be a genetic isomorph (it’s growing on me) but getting closer and closer to the target species. Is there any point at which we can say – OK, this is basically a dire wolf?

It’s also important to recognize that species are not discrete things. They are temporary dynamic and shifting islands of interbreeding genetic clusters. We should also not confuse taxonomy for reality – it is a naming convention that is ultimately arbitrary. Cladistics is an attempt to have a fully objective naming system, based entirely on evolutionary branching points. However, using that method is a subjective choice, and even within cladistics the break between species is not always clear.

I find this all pretty exciting. I also think the technology can be very important. Its best uses, in my opinion, are to de-extinct (as close as possible) recently extinct species due to human activity, ones where there is still something close to their natural ecosystem still in existence (such as the dodo and thylacine). Also it can be used to increase the genetic diversity of endangered species and reduce the risk of extinction.

Using it to bring back extinct ancient species, like the mammoth and dire wolf (or non-avian dinosaurs, for that matter), I see as a research project. And sure, I would love to see living examples that look like ancient extinct species, but that is mostly a side benefit. This can be an extremely useful research project, advancing our understanding of genetics, cloning and genetic engineering technology, and improving our understanding of ancient species.

This recent controversy is an excellent opportunity to teach the public about this technology and its implications. It’s also an opportunity to learn about categorization, terminology, and evolution. Let’s not waste it by overreacting to the hype and being dismissive.

The post OK – But Are They Dire Wolves first appeared on NeuroLogica Blog.

Five months ago, I called RFK Jr. an "extinction-level" threat to US biomedical science and public health. That extinction is under way.

The post How bad is it? RFK Jr.’s extinction-level threat to science-based federal health policy and public health is here first appeared on Science-Based Medicine.

Whether your views on climate change are informed by politics or science, it's getting harder to ignore it's effects on our lives down here on Earth. But a surprising study reports that increasing concentrations of greenhouse gases in our atmosphere could also be affecting the problem of space junk. As the heat energy stored in our atmosphere increases, its ability to scrub debris from Low-Earth Orbit (LEO) decreases, increasing the risk of satellite collisions and making it more likely that humanity could lose access to space entirely.

One of the challenges of searching for life in the Universe is that there is no single universal biosignature that could reveal its presence. Even if we could tell the difference between chemicals produced by living organisms and those from non-living sources like volcanoes, we're still making the assumption that alien life would resemble life on Earth. A new paper proposes that missions search for “energy-ordered resource stratification” which only happens when both self-replication and ecological competition are present.

TikTok Flat Earthers; News Items: De-extincting the Dire Wolf, What Experts Think About AI, Planned Obsolescence, VR Touch Sensory; Who's That Noisy; Your Questions and E-mails: SNPs vs Sequencing; Science or Fiction

I remind you once again to send in your photographs as there’s always a need. Thanks!

Today we have some pictures taken by James Blilie and his son Jamie. The captions are indented, and you can enlarge the photos by clicking on them.

Here is a set of photos from our local area.  We live in far southern Washington state in Klickitat County.  These photos are from Klickitat and Skamania Counties.

A mostly full moon photographed on February 8, 2025:

Two views of Mount Adams from the front porch on our new (2024) home.  Both are taken at sunset.  One is a black and white closeup.  The other also shows our local gang of Black-tailed deer (Odocoileus hemionus columbianus).  Mount Adams is about 20 miles directly north of our house:

The next shot shows left to right:  Mount Adams, Mount Rainier, and the Goat Rocks Wilderness from the top of a local ridge.  I took this on March 1, 2025:  It was 60°F (16°C) and sunny, unusual for the first of March!  The view is well worth the work on this hike:

The next bunch of photos were taken at the Wind River Arboretum in Skamania County, definitely on the wet (west) side of the Cascade Range.

A cross-section of the purportedly largest Douglas Fir (Pseudotsuga menziesii) found in Washington state and the placard that accompanies it.  The section was taken at 60-feet (18m) above the ground and the tree was determined to be 393-feet (120m) tall:

[JAC: I can’t help pointing out the superfluous apostrophe in the park sign below.]

Western Red Cedar (Thuja plicata):  Foliage and a (small) example tree:

Two shots by our son Jamie of Bird’s Nest Fungus (Nidulariaceae spp.):

Last year’s Bracken Fern (Pteridium aquilinum), also taken by Jamie:

Views of Sword Ferns (Polystichum munitum), also taken by Jamie:

Equipment:

Mine:

Olympus OM-D E-M5 camera (micro-4/3, crop factor = 2.0)
LUMIX G X Vario, 12-35MM, f/2.8 ASPH lens
LUMIX 35-100mm  f/2.8 G Vario lens
LUMIX G Vario 7-14mm  f/4.0 ASPH lens
LUMIX G Vario 100-300mm F/4.0-5.6 MEGA O.I.S. lens

Jamie’s:

Nikon D5600 (crop factor = 1.5)
Nikkor AF-P DX 18-55mm f/3.5-5.6 G VR lens
Sigma 150-600mm f/5.0-6.3 DG OS HSM lens

The US Defense Advanced Research Projects Agency (DARPA) wants to know which of the quantum computers now in development have the best chance of being game-changing technologies

New data establish an upper limit of 0.45 eV/c2 (equivalent to 8 x 10-37 kilograms) for the neutrino mass. KATRIN measures neutrino mass in the laboratory using a model-independent method.

Researchers have developed a pioneering, sustainable method for producing cadmium-based quantum dots (QDs) in water using a biocompatible chalcogen source. This fully aqueous, continuous flow process avoids harmful organic solvents and offers enhanced safety, scalability, and environmental performance. A collaboration led to the creation of a water-soluble chalcogen transfer agent inspired by peptide chemistry. Real-time Raman spectroscopy enabled detailed analysis of reaction mechanisms. The new system improves productivity while reducing waste and energy use. Although cadmium QDs are efficient, their toxicity remains a concern, prompting the team to explore greener alternatives. This innovation marks a significant step toward responsible, large-scale nanomaterial production.

Researchers have developed a pioneering, sustainable method for producing cadmium-based quantum dots (QDs) in water using a biocompatible chalcogen source. This fully aqueous, continuous flow process avoids harmful organic solvents and offers enhanced safety, scalability, and environmental performance. A collaboration led to the creation of a water-soluble chalcogen transfer agent inspired by peptide chemistry. Real-time Raman spectroscopy enabled detailed analysis of reaction mechanisms. The new system improves productivity while reducing waste and energy use. Although cadmium QDs are efficient, their toxicity remains a concern, prompting the team to explore greener alternatives. This innovation marks a significant step toward responsible, large-scale nanomaterial production.