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亓官先生
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胡卜凱

我是物理系畢業生,有了自然科學的基本常識;容易讀懂科學新知的報導,同時也有興趣接觸它們。

過去《中華雜誌》雖是政論性和人文學術性刊物,但有時會介紹一些自然科學的研究結果;每年也都會刊登有關諾貝爾獎得主的消息。我唸大學時就替《中華》翻譯過一篇報導天文學脈動星的文章。

同窗好友王家堂兄在1980前後,介紹我進入高能物理的「普及科學」世界;此後常常讀一些這方面的書籍。因此,我一直保持著對物理學的興趣,之後自然而然的進入宇宙學領域。

以上三點是這個部落格過去經常轉載自然科學方面報導/論文的背景。



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另一個修正演化論企圖的盲點 - Jerry Coyne
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廓因教授這篇文章批評婁博教授的觀點後者請見本欄2024/02/14的貼文廓因教授是生物學家內容自然充實有料。熟悉相關領域的網友可以慢慢品味。我的《短評》則針對婁博教授「論述前提」(本2024/02/15貼文)

如我指出,婁博教授的許多思考盲點來自他具有爭議「論述前提」所導致的「認知偏差」廓因教授似乎苟同我的看法例如下文中這段話This is a matter of ignorance that will eventually be solved.”和我《短評》中1.1小節最後一段文字是同樣的意思。其次廓因教授也批評了我提到婁博教授目的論」傾向


Yet another misguided attempt to revise evolution

Jerry Coyne, 02/12/24

What we have below (click on headline for free access) is a review in Nature by Denis Noble of a new book by Philip BallHow Life Works: A User’s Guide to the New Biologywhich has garnered good reviews and is currently #1 in rankings of books on developmental biology.  The Amazon summary promises that the book will revise our view of life:

A cutting-edge new vision of biology that will revise our concept of what life itself is, how to enhance it, and what possibilities it offers.

Biology is undergoing a quiet but profound transformation. Several aspects of the standard picture of how life works—the idea of the genome as a blueprint, of genes as instructions for building an organism, of proteins as precisely tailored molecular machines, of cells as entities with fixed identities, and more—have been exposed as incomplete, misleading, or wrong.. . .

I haven’t read it yet, though I will (I have several books ahead of it, including the galleys of Richard Dawkins’s new book, for which I’m to provide a blurb (“
正面的簡介,摘要). Instead, I will review a review: Denis Noble’s review published a few days ago. (That’s the screenshot below. 請至原網頁查看;該文即《自然科學:普及篇2024/02/14貼文) Admittedly, it’s a review of a review, but Noble gives his take on the book’s importance, and in so doing reveals his own idea that neo-Darwinism is not only impoverished, but misguided in important ways.  And, as usual, Noble proves himself misguided.

In some ways it’s unfortunate that Noble was chosen as a reviewer, as the man, while having a
sterling reputation in physiology and systems biology, is largely ignorant of neo-Darwinism, and yet has spent a lot of the last decade trying to claim that neo-Darwinism is grossly inadequate to explain the features and evolutionary changes of organisms. You can see all my critiques of Noble here, but I’ll just quote briefly from the latest to give you a flavor of how he attacks modern evolutionary theory:

In an earlier post I wrote, “
Famous physiologist embarrasses himself by claiming that the modern theory of evolution is in tatters“, I emphasized five assertions Noble made in a 2013 paper in Experimental Physiology, and then I criticized them as being either deeply misguided or flat wrong. Noble’s claims:

*  Mutations are not random
*  Acquired characteristics can be inherited
*  The gene-centered view of evolution is wrong [This is connected with #2.]
*  Evolution is not a gradual gene-by-gene process but is macromutational.
*  Scientists have not been able to create new species in the lab or greenhouse, and we haven’t seen speciation occurring in nature.

I then
assessed each claim in order:

*  Wrong, partly right but irrelevant, wrong, almost completely wrong, and totally wrong (
speciation is my own area).
*  And yet Noble continues to bang on about “the broken paradigm of Neo-Darwinism,” which happens to be the subtitle of his new article (below) in 
IAI News, usually a respectable website run by the Institute of Art and Ideas.  

And yes, Noble’s banging persists in his review of Ball’s book. The criticisms I level will be against Noble’s claims, as I can’t verify whether he’s accurately characterizing Ball’s views or spouting his (Noble’s) own misguided views.

The problem with Noble;s review is twofold: the stuff he says is new and revolutionary is either old and well known, or it’s new and
unsubstantiated.  Here are a few of his quotes (indented “以下以*號顯示” and in italics) and my take (flush left):

First, Noble’s introduction to the book, which is okay until Noble tries to explicate it:

*  So long as we insist that cells are computers and genes are their code,” writes Ball, life might as well be “sprinkled with invisible magic”. But, reality “is far more interesting and wonderful”, as he explains in this must-read user’s guide for biologists and non-biologists alike.

On to Noble’s asseverations:

*  When the human genome was sequenced in 2001, many thought that it would prove to be an ‘instruction manual’ for life. But the genome turned out to be no blueprint. In fact, most genes don’t have a pre-set function that can be determined from their DNA sequence.

Well, the genome
 is more or less a blueprint for life, for it encodes for how an organism will develop when the products of its genome, during development, interact with the environment—both internal and external—to produce an organism. Dawkins has emphasized, though, that the genome is better thought of as “recipe” or “program” for life, and his characterization is actually more accurate (you can “reverse engineer” a blueprint from a house and engineer a house from a blueprint—it works both ways—but you can’t reverse engineer a recipe from a cake or a DNA sequence from an organism.)  The DNA of a robin zygote in its egg will produce an organism that looks and behaves like a robin, while that of a starling will produce a starling.  You can’t change the environment to make one of them become the other. Yes, the external environment (food, temperature, and so on) can ultimately affect the traits of an organism, but it is the DNA itself, not the environment, that is the thing that changes via natural selection. It is the DNA itself that is passed on, and is potentially immortal. And the results of natural selection are coded in the genome. (Of course the “environment” of an organism can be internal, too, but much of the internal environment, including epigenetic changes that affect gene function are themselves coded by the DNA.)

As for genes not having a “pre-set function that can be determined from their DNA sequence,” this is either wrong or old hat.  First, it is true that at this point we don’t always know how a gene
functions from its DNA sequence alone, much less how it could change the organism if it mutates. This is a matter of ignorance that will eventually be solved. As for “pre-set function”, what does Noble mean by “pre-set”?  A single gene can participate in many developmental pathways, and if it mutates, it can change development in unpredictable ways, and in ways you couldn’t even predict from what that gene “normally” does. The gene causing Huntington’s chorea, a fatal neurodegenerative disease, has a function that’s largely unknown but is thought to affect neuron transport. But it also has repeated sections of the DNA (CAGCAGCAG. . . . .), and mutations that increase the number CAG repeats can cause the disease when they exceed a certain threshold.

But the “Huntington’s gene” is not there to cause disease, of course. It interacts with dozens or even hundreds of other genes in ways we don’t understand. What is its “pre-set” function? The question is
meaningless. And was does “pre-set” mean, anyway?

The second sentence in the bit above is garbled and ambiguous, and at any rate doesn’t refute the notion that the genome is indeed the “instruction manual for life.”

But wait: there’s more!

*  Instead, genes’ activity — whether they are expressed or not, for instance, or the length of protein that they encode — depends on myriad external factors, from the diet to the environment in which the organism develops. And each trait can be influenced by many genes. For example, mutations in almost 300 genes have been identified as indicating a risk that a person will develop schizophrenia.
It’s therefore a huge oversimplification, notes Ball, to say that genes cause this trait or that disease. The reality is that organisms are extremely robust, and a particular function can often be performed even when key genes are removed. For instance, although the HCN4 gene encodes a protein that acts as the heart’s primary pacemaker, the heart retains its rhythm even if the gene is mutated.

Polygeny,” or the view that traits can be affected by many genes, is something I learned in first-year genetics in 1968. But some “traits” or diseases are the product of single genes, like the trait of getting Huntington’s Chorea of sickle-cell disease.  But many diseases, like high blood pressure and heart disease, can be caused by many genes. And it’s not just diseases. Whether your earlobes are attached to your face or are free is based on a single gene, and eye color, to a large extent, is too (see this list for other single-gene alternative traits).

As far as the HCN4 gene goes, mutations may allow it to have a rhythm, but many mutations in that gene cause abnormal rhythms.and can even bring on death through heart attacks. No, the gene is not robust to mutations, and I can’t understand where Noble’s statement comes from. It appears to be wrong. (I am not attributing it to Ball here.)

More:

*  Classic views of evolution should also be questioned. Evolution is often regarded as “a slow affair of letting random mutations change one amino acid for another and seeing what effect it produces”. But in fact, proteins are typically made up of several sections called modules — reshuffling, duplicating and tinkering with these modules is a common way to produce a useful new protein.

This is not a revision of the “classic” view of evolution because we’ve known about
domain-swapping for some time. For example, the “antifreeze” proteins of Arctic and Antarctic fish can involve changes in the number of repeats in the enzyme trypsinogen, which normally has nothing to do with preventing freezing. Or, antifreeze proteins can arise via the cobbling together of bits of different known genes, or from bits of the unknown genes, or even be transferred via horizontal acquisition from other species.  Yes, this happens, but it’s not the only way by a long shot that evolution occurs. In fact, now that we can sequence DNA, we’ve found that many adaptive changes in organisms are based in changes in single genes or their regulatory regions, and not swapping of modules. Here’s a figure from a short and nice summary by Sarah Tishkoff from 2015 showing single genes involved in various adaptations that have occurred in one species—our own. The traits are given at the top, and the genes involved are by the symbols. For example, though several genes can involve skin pigmentation, mutations in just one of them can make a detectable change.

Global distribution of locally adaptive traits. Adaptation to diverse environments during human evolution has resulted in phenotypes that are at the extremes of the global distribution. Fumagalli et al. have integrated scans of natural selection and GWAS to identify genetic loci associated with adaptation to an Arctic environment. ILLUSTRATION: A. CUADRA/SCIENCE AND MEAGAN RUBEL/UNIV. OF PENNSYLVANIA (請至原網頁查看圖片)

At any rate, we can nevertheless regard shuffling of domains (or even horizontal gene transfer from other species) as mutations, and the new mutated gene then evolves according to its effect on the replication of the gene. No revision of neo-Darwinism or its mathematics is involved. New ways of changing genes haven’t really revised our view of how evolution works, even when we’re talking about the “
neutral theory” instead of natural selection.

These mutations, by the way, contra Noble, are still “
random”—that is, they occur irrespective of whether they’d be useful in the new environment—and although they can make big changes in the organism’s physiology or appearance, can nevertheless evolve slowly.  A gene with a big effect need not evolve quickly, for the rate of evolution depends not on the effect on the organism’s appearance, physiology, and so on, but on its effect on the organisms’s reproductive capacity. And these things need not be correlated.

*  Later in the book, Ball grapples with the
philosophical question of what makes an organism alive. Agency — the ability of an organism to bring about change to itself or its environment to achieve a goal — is the author’s central focus. Such agency, he argues, is attributable to whole organisms, not just to their genomes. Genes, proteins and processes such as evolution don’t have goals, but a person certainly does. So, too, do plants and bacteria, on more-simple levels — a bacterium might avoid some stimuli and be drawn to others, for instance. Dethroning the genome in this way contests the current standard thinking about biology, and I think that such a challenge is sorely needed.

*  Ball is not alone in calling for a drastic rethink of how scientists discuss biology. There has been a flurry of publications in this vein in the past year, written by me and others
24. All outline reasons to redefine what genes do. All highlight the physiological processes by which organisms control their genomes. And all argue that agency and purpose are definitive characteristics of life that have been overlooked in conventional, gene-centric views of biology.  

This passage verges on the
teleological.  For surely organisms don’t havegoals” when they evolve.  If a mutation arises that increases the rate of replication of a gene form (say one increasing tolerance to low oxygen in humans living in the Himalaya), it will sweep through the population via natural selection. If it reduces oxygen binding, it will be kicked out of the population. Can we say that increased oxygen usage is a “goal”? No, it’s simply what happens, and I suspect there are other ways to adapt to high altitude, like getting darker skin. To characterize organisms as evolving to meet goals, as Noble implies here, is a gross misunderstanding of the process.

Yes, the organism is the “
interactor”, as Dawkins puts it: the object whose interaction with its environment determines what gene mutations will be useful. But without the “replicator”—the genes in the genome—evolution cannot occur.  The whole process of adaptation, involving the interaction of a “random” process (mutation) and a “deterministic” one (natural selection), is what produces the appearance of purpose. But that doesn’t mean, at least in any sense with which we use the word, that “purpose” is what makes organisms alive.

But the appearance of “purpose” as a result of natural selection brings up another point, one that Dawkins makes—or so I remember.  I believe that he once defined life as “those entities that evolve by natural selection.”  I can’t be sure of that, but it’s as good a definition of life as any, as it involves organisms having
replicators, interacting “bodies”, and differential reproduction. (According to that definition, by the way, viruses are alive.)  So if you connect natural selection with purpose, one might say, “Life consists of those organisms who have evolved to look as if as if they had a purpose.”  But I prefer Dawkins’s definition because it’s more fundamental.

At the end, Noble says that this “new view of life” will help us cure diseases more readily:

This burst of activity represents a frustrated thought that “it is time to become impatient with the old view”, as Ball says. Genetics alone cannot help us to understand and treat many of the diseases that cause the biggest health-care burdens, such as schizophrenia, cardiovascular diseases and cancer. These conditions are physiological at their core, the author points out — despite having genetic components, they are nonetheless caused by cellular processes going awry. Those holistic processes are what we must understand, if we are to find cures.

I haven’t heard anybody say that “genetics alone can help us treat complex diseases”. You don’t treat heart disease by looking for genes (though you can with some cancers.) But genetics can surely help! For genetic engineering is on the way, and at least some diseases, like sickle-cell anemia, will soon be “curable” by detecting the mutated genes in embryos or eggs and then fixing the mutation with CRISPR. And advances in genetics are surely helping us cure cancer—see 
this article.  But of course some diseases, even those with a genetic component, need environmental interventions: so called “holistic” cures. There may, for example, be a genetically-based propensity to get strep throat. But if you get it, you don’t worry about genes, you take some penicillin or other antibiotic. (Curiously, the form of Streptococcus that causes strep throat doesn’t seem to have evolved resistance to the drug!)

Overall, I don’t see much new in Noble’s take on evolution—just a bunch of puffery and regurgitation of what we already know. Perhaps people need to know about this stuff in a popular book, but, after all, Noble’s piece was written for scientists, for it appears in Nature.

Despite repeated claims in the last few years that neo-Darwinism is moribund or even dead, it still refuses to lie down. Happy Darwin Day!

Addendum by Greg Mayer: For those interested in the distinction between the blueprint (wrong) and recipe (on the right track) analogies for the genome, I wrote a post explicating the difference, citing and quoting Richard, here at WEIT; the post also explains why the Wikipedia article about “Epigenetics” is definitionally wrong; see especially the link to this
 paper by David Haig.

Development is epigenetic

by Greg Mayer One of the points I stress to students in my evolution class is that development is epigenetic: organisms develop from a less differentiated state to a more differentiated state. In modern terms, genes, the intraembryonic environment, and the extraembryonic environment interact to produce the organism through a sequence of stages going from an undeveloped to a mature state. . .

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《基因並非生物成長的藍圖》短評
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0.  前言

這篇文章有論點,但也相當有趣(請見本欄上一篇)。前者指婁博教授提出了他的主張,也列舉了支持他這些主張的依據;後者指婁博教授的文章有濃厚的哲學意味,卻不幸包含了至少兩個邏輯謬誤。略抒拙見於下。

1.  哲學立場

這篇文章不到1,000字,婁博教授把重點放在生物學和基因學的相關論述;對他立論背後的哲學立場僅僅一筆帶過;後者請參考上一節關於他生平超連接中的簡短介紹。

1.1
綜觀論

婁博教授的綜觀論傾向可從原文倒數第二段中,他使用了holistic processes” 一詞看出這個立場通常跟構成論相對。我並不排斥綜觀論,尤其在社會科學理論及其應用上;但就我略有所知的自然科學各領域而言,我都傾向構成論

婁博教授在本文中沒有提到另一個相關領域環境遺傳學(或稱擬遺傳學);這個領域可參見環遺學1環遺學2

我認為綜觀論和綜合性質論兩者,是目前人類還沒有掌握到全部知識前的過渡理論;也就是說,在我們沒有能力以現有理論解釋某些現象前,一種類似OK繃功能的觀點

1.2
目的論

婁博教授的目的論傾向可從以下兩段文字看出

“Genes, proteins and processes such as evolution don’t have goals, but a person certainly does.”  

這句話是原書作者博爾教授的文字婁博教授認同並引用

“… And all argue that
agency and purpose are definitive characteristics of life that have been overlooked in conventional, gene-centric views of biology.”

對「目的論」有興趣的朋友,請參考此文

在以上引用的第二段文字中有「行動能力」一詞,此概念的用法可參見我剛發表的我對「文革/紅衛兵」的看法(該文第2.1小節)

我認為一般來說,自然、社會、和人文三大科學領域中的「目的論」都站住腳但是,每一個人在她/他的生命歷程中,可以選擇/改變自己生活的「目的」這個立場來自我所了解的意識自由意志與「行動能力(特別是該欄《主動性》一文)

2.
邏輯謬誤

1)  前後矛盾

請比較這三段文字

a.  “Genes, proteins and processes such as evolution don’t have goals, …”
b.  “… reshuffling, duplicating and tinkering with these modules is a common way to produce a useful new protein.”
c.  “… organisms control their genomes.”

分析如下

b
段的to produce a useful new protein.” ”useful new protein” 應該解讀為一種goal” b段與a段矛盾

c
段中的organisms” 一字,依脈絡應該解讀為”genes” 或相應的人體結構/組成物質,而不是指「人」「控制」蘊含「目的」;因此c段也與a段矛盾

2)  結論不能從前提導出

請參考以上我對綜觀論以及目的論的一般性批評

婁博教授今年88歲,且不論他注意力或關照力是否已經難以周全;從他執著於上述的「哲學立場」來看,其思路中多多少少有些「認知偏差」也就不足為怪了

3. 
結論

雖然婁博教授引用了一些研究報告支持他的論點,整篇文章的嚴謹度和說服力不足

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基因並非生物成長的藍圖 ---- Denis Noble
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(請參見本欄下一篇《短評》)


t’s time to admit that genes are not the blueprint for life

The view of biology often presented to the public is oversimplified and out of date. Scientists must set the record straight, argues a new book.

Denis Noble, 02/05/24

How Life Works: A User’s Guide to the New Biology, Philip Ball, Pan Macmillan (2024)

For too long, scientists have been content in espousing the lazy metaphor of living systems operating simply like machines, says science writer Philip Ball in How Life Works. Yet, it’s important to be open about the complexity of biology — including what we don’t know — because public understanding affects policy, health care and trust in science. “So long as we insist that cells are computers and genes are their code,” writes Ball, life might as well be “sprinkled with invisible magic”. But, reality “is far more interesting and wonderful”, as he explains in this must-read user’s guide for biologists and non-biologists alike.

When the human genome was sequenced in 2001, many thought that it would prove to be an ‘instruction manual’ for life. But the genome turned out to be no blueprint. In fact, most genes don’t have a pre-set function that can be determined from their DNA sequence.

Instead, genes’ activity — whether they are expressed or not, for instance, or the length of protein that they encode — depends on myriad external factors, from the diet to the environment in which the organism develops. And each trait can be influenced by many genes. For example, mutations in almost 300 genes have been identified as indicating a risk that a person will develop schizophrenia.

It’s therefore a huge oversimplification, notes Ball, to say that genes cause this trait or that disease. The reality is that organisms are extremely robust, and a particular function can often be performed even when key genes are removed. For instance, although the HCN4 gene encodes a protein that acts as the heart’s primary pacemaker, the heart retains its rhythm even if the gene is mutated1.

Another metaphor that Ball criticizes is that of a protein with a fixed shape binding to its target being similar to how a key fits into a lock. Many proteins, he points out, have disordered domains — sections whose shape is not fixed, but changes constantly.

This “fuzziness and imprecision” is not sloppy design, but an essential feature of protein interactions. Being disordered makes proteins “versatile communicators”, able to respond rapidly to changes in the cell, binding to different partners and transmitting different signals depending on the circumstance. For example, the protein aconitase can switch from metabolizing sugar to promoting iron intake to red blood cells when iron is scarce. Almost 70% of protein domains might be disordered.

Classic views of evolution should also be questioned. Evolution is often regarded as “a slow affair of letting random mutations change one amino acid for another and seeing what effect it produces”. But in fact, proteins are typically made up of several sections called modulesreshuffling, duplicating and tinkering with these modules is a common way to produce a useful new protein.  

Later in the book, Ball grapples with the philosophical question of what makes an organism alive. Agency — the ability of an organism to bring about change to itself or its environment to achieve a goal — is the author’s central focus. Such agency, he argues, is attributable to whole organisms, not just to their genomes. Genes, proteins and processes such as evolution don’t have goals, but a person certainly does. So, too, do plants and bacteria, on more-simple levels — a bacterium might avoid some stimuli and be drawn to others, for instance. Dethroning the genome in this way contests the current standard thinking about biology, and I think that such a challenge is sorely needed.

Ball is not alone in calling for a drastic rethink of how scientists discuss biology. There has been a flurry of publications in this vein in the past year, written by me and others24. All outline reasons to redefine what genes do. All highlight the physiological processes by which organisms control their genomes. And all argue that agency and purpose are definitive characteristics of life that have been overlooked in conventional, gene-centric views of biology.

This burst of activity represents a frustrated thought that “it is time to become impatient with the old view”, as Ball says. Genetics alone cannot help us to understand and treat many of the diseases that cause the biggest health-care burdens, such as schizophrenia, cardiovascular diseases and cancer. These conditions are physiological at their core, the author points out — despite having genetic components, they are nonetheless caused by cellular processes going awry. Those holistic processes are what we must understand, if we are to find cures.

Ultimately, Ball concludes that “we are at the beginning of a profound rethinking of how life works”. In my view, beginning is the key word here. Scientists must take care not to substitute an old set of dogmas with a new one. It’s time to stop pretending that, give or take a few bits and pieces, we know how life works. Instead, we must let our ideas evolve as more discoveries are made in the coming decades. Sitting in uncertainty, while working to make those discoveries, will be biology’s great task for the twenty-first century. 

Nature 626, 254-255 (2024)
doi: https://doi.org/10.1038/d41586-024-00327-x

References

Noble, D. Prog. Biophys. Mol. Biol. 166, 3–11 (2021)., Article PubMed Google Scholar 

Noble, R. & Noble. D. Understanding Living Systems (Cambridge Univ. Press, 2023)., Google Scholar 
Vane-Wright, R. I. & Corning, P. A. Biol. J. Linn. Soc. 139, 341–356 (2023)., Article Google Scholar 
Corning, P. A. et al. (eds) Evolution “On Purpose”: Teleonomy in Living Systems (MIT Press, 2023)., Google Scholar 

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10個科學家目前還沒有答案的問題 -- Marcelo Gleiser
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10 of the most mystifying open questions in science

From how life emerged on Earth to why we dream, these unanswered questions continue to perplex scientists.

Marcelo Gleiser, 12/21/23

KEY TAKEAWAYS

*  With the end of 2023 approaching, it’s time to revisit some of the toughest questions in science.
*  Here's my (admittedly biased) list of the top ten. Each entry is briefly explained and accompanied by references to current books and articles on the topics. 
*  As you'll see, some of these questions have been with us for quite some time, and they may be unanswerable — at least through the usual scientific methodology.

To celebrate (with a sigh perhaps?) the end of this turbulent year, there’s nothing better than diving into some of the biggest open questions in science — those that have long kept scientists up at night. Though confounding, these questions point to an essential fact in science: 
the more we know, the more there is to know. There is no end to knowledge as long as we keep asking questions (and receive funding to try to answer them). Even more interestingly, some of these questions simply can’t be answered, at least not through the usual scientific methodology that combines objectivity and reductionism: the notions, respectively, that we can separate ourselves from the objects we are studying, and that it is possible to break complex systems into smaller ones to study their behavior and then infer the behavior of the whole from the behavior of the parts.

Every list of “most important” questions has a dose of arbitrariness, given the author’s subjectivity. However, I would venture to say that these rank among the toughest open questions — and for sure among the more mysterious and attention-grabbing. So, here it goes, in no particular order:

1. What is the Universe made of? We know only 5% of the composition of the Universe. This 5% is made of the familiar atoms of the periodic table, their molecular aggregates, or the components of the atoms: protons, electrons, and neutrons. There are also neutrinos — the elusive particles that can traverse matter as if nothing was there, including the whole of Earth. 
The mystery is the other 95%, composed of dark matter (roughly 27%) and dark energy (roughly 68%). Dark matter doesn’t shine and is found around galaxies and clusters of galaxies, like an invisible cloak. We know it’s there because it has mass and hence gravity: It pulls on the familiar 5% we can see, and we can measure this effect. Dark energy is much more mysterious, an ether-like medium filling up space with the bizarre property of pushing it apart, making galaxies accelerate away from one another. We don’t know what dark matter or dark energy are, and there are hypothetical explanations that try to modify Einstein’s theory of gravity to accommodate the observations and do away with the darkness. But after decades of searching, we remain quite ignorant.

2. How did life come about? Life appeared on Earth some 3.5 billion years ago, perhaps earlier. The mystery here is how aggregates of nonliving atoms gathered into progressively more complex molecules that eventually became the first living entity, a chemical machine capable of metabolism and reproduction. The fact that living matter is 
matter with intentionality remains a profound mystery.

3. Are we alone in the Universe? This question is really two questions, given that we want to know not only whether any extraterrestrial life exists but also whether it is intelligent. Ultimately, 
we would like to know how common life is. We also need to know why, if intelligent life is not so rare, we haven’t yet heard from “them”? On the question of aliens, I recommend the recent book by Big Think columnist Adam Frank, The Little Book of Aliens, for an up-to-date synopsis of the search for life in the cosmos. As I pointed out in my recent book, this question has a direct impact on how we relate to our own future and the planet we call home.

4. What makes us human? We have three times more neurons than a gorilla, but our DNAs are almost identical. Many animals have a rudimentary language, can use tools, and recognize themselves in mirrors. So, what exactly differentiates us from them? The thicker frontal cortex? The opposing thumb? The discovery of fire and the ability to cook? Our culture? When did language and tool-making appear? An excellent intro to this is Jeremy DeSilva’s book, 
First Steps.

5. What is consciousness? We’ve confronted this question before in 
these pages, wondering about the nature of consciousness, and even its possible connection with quantum physics, a trendy topic in some circles. How is it that the brain generates the self of self, the unique experience that we have of being unique? Can the brain be reversed-engineered to be modeled by machines or is this a losing proposition? And why is there a consciousness at all? What is its evolutionary purpose, if any?

6. Why do we dream? Even though we spend about a third of our lives sleeping, we still don’t know why we dream. Do dreams have an essential function, physiological and/or psychological? Or are they simply random images of a brain in partial rest? Was Freud right about his theory that dreams are some sort of expression of repressed desires? Or is that all bogus?

7. Why does matter exist? According to the laws of physics, 
matter shouldn’t exist on its own; each particle of matter — each electron, proton, neutron — should have a companion of antimatter, like twins. So, there should be positrons, antiprotons, and antineutrons in abundance. But there aren’t. The problem is that when matter and antimatter meet, they disintegrate in a puff of high-energy radiation. If you shook hands with your antimatter other, a good chunk of the U.S. would blow up in smoke. So, the mystery is what happened to this antimatter. Clearly, if the Universe had equal amounts of both earlier on, something happened to favor matter over antimatter. What? Was the Universe “born” this way, with a huge asymmetry between matter and antimatter? Maybe some primordial asymmetry evolved to do the job, selecting matter? If so, when did it act in cosmic history, and what would this asymmetry be? We’ve been trying to figure this one out for decades with no great success.

8. Are there other universes? Or is our Universe the only one? Believe it or not, modern theories of cosmology and particle physics predict the existence of other universes, potentially with different properties to our own. Are they there? How would we know, if we could? If we can’t confirm this hypothesis, is it still part of science? 
I have argued here before that the multiverse hypothesis is profoundly problematic and not particularly useful, even if fun to think about.

9. Where will we put all the carbon? With the global vamping up of industrialization, we are putting more and more carbon (and methane) up in the atmosphere, accelerating global warming. 
What can be done to change our impact on the environment? And what happens if we don’t? Models of global warming offer a range of predictions, from somewhat mild to dire. But clearly, time is running out to ponder about the issue and do nothing. It’s time to take this seriously at a global scale, for the benefit of the next generation and even just the next decade or so. Politicians are moving too slowly. We need to take this one into our own hands and act individually as well.

10. How can we get more energy from the Sun? We have based our explosive growth mainly on fossil fuels. Nevertheless, we have a remarkable energy source up in the sky, waiting to be explored more efficiently. Also, can we reproduce the solar engine here on Earth, fusing hydrogen into helium in a controllable and viable way to solve the energy problem for the foreseeable future? 
Progress is coming, but slower than we’d like. Or need.


What was it like when the very first stars died?

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The Ten Most Significant Science Stories of 2023

From an asteroid sample that was delivered to Earth to a discovery about human migration from North America, these were the biggest moments of the year

Carlyn Kranking/Joe Spring, 12/20/23

In 2023, a whirlwind of science headlines swept across our screens, from the find that our ancestors nearly went extinct 900,000 years ago to the discovery of a brilliant green comet in the sky. In major health news, the coronavirus public health emergency expired, and the disease took up less of our attention, though it continued to have disastrous impacts. Medical experts are anticipating updated annual vaccines will be released to continue fighting the virus as it evolves.

Also evolving rapidly this year was artificial intelligence, which found uses in everything from medicine to wildlife biology. In one innovative application, it was used to help forecast when birds took to the skies. Such an ability can help officials determine when to turn off building lights to prevent bird strikes—a conservation strategy that made national news when almost 1,000 birds died in one night after hitting a single lakeside building in Chicago.

That was a grim stat, but the year was filled with amazing news as well, including the astounding images released by the James Webb Space Telescope. In major math news, researchers found a shape with a pattern that never repeats. And in France, scientists discovered that arresting patterns left in rock are the oldest known Neanderthal cave engravings.

Unfortunately, but not unexpectedly, climate change continued to generate plenty of headlines, as the year became the hottest on record. Amid intensifying natural disasters, world leaders gathered in Dubai, United Arab Emirates, for the 28th United Nations Climate Change Conference, or COP28. While the proceedings closed with a landmark deal that made the first-ever global commitment to transition away from fossil fuels, several experts criticized the text for not going far enough.

While we were riveted by all of those stories and more, only some made our list of the biggest science events and discoveries this year. Plenty of amazing new findings surely await us in 2024, but before we cover them, here’s a look back at the moments that shaped 2023 as another major year in science.

Archaeologists find ancient Native Americans crossed back over to Asia

Between 20,000 and 30,000 years ago, hunter-gatherers from eastern Eurasia likely ventured over to North America across the Bering Strait. But research this year suggests they and their descendants didn’t make a one-way trip. Several times in history, ancient Native Americans made their way back across the strait to Eurasia, according to a study published in Current Biology in January. Researchers recovered ancient DNA from ten Eurasian individuals who lived 500 to 7,500 years ago. Their analysis shows that humans with Native American lineages traveled as far away as Kamchatka and central Siberia, likely returning from North America to Asia roughly 5,000 years ago.

The find was one of many interesting discoveries related to ancient migrations and the Americas this year. In July, a study published in Proceedings of the Royal Society B described three pendants in Brazil made from sloth bones that date to between 25,000 and 27,000 years before present. That find supports the theory that humans made it to the Americas earlier than previously thought. (For many decades, researchers thought humans traveled from Russia to Alaska roughly 15,000 years ago.) And in an October study published in Science, an analysis of evidence found near fossilized footprints in New Mexico suggests that the imprints date to 23,000 years ago, which also supports the idea of an earlier migration of humans to North America. While the timeline of migrations to the Americas—and back—continues to be debated, many sites that will offer more clues await discovery and analysis. —Joe Spring

Artificial intelligence yields scientific breakthroughs as experts call for caution

2023 was a “breakout year” for artificial intelligence. Following the release of OpenAI’s ChatGPT at the end of 2022, machine learning has increasingly been in the public eye. A.I. made its way into courtroomsmusic and art this year, raising a slew of ethical concerns. In the realm of science, the cutting-edge technology is paving the path toward new discoveries and more advanced processing of data.

Several groups of researchers experimented with having A.I. algorithms generate wordsimages and even music based on people’s brain scans—a technique that, down the line, could help stroke patients and paralyzed people to communicate by thinking. Machine learning has helped in conservation, such as by tracking migrating birds—the A.I.-powered tool BirdCast can alert people to an incoming wave of migrants, which may help prevent disease, inform Lights Out programs to reduce window strikes, and tip off birders about flocks in their area. Scientists are also developing A.I. tools that can identify species based only on a photograph, distinguish between similar-looking mushrooms or pinpoint a bird species from its song. And, inspired by the way ChatGPT follows patterns in language to generate words, researchers have experimented with translating whale sounds using A.I.

At the same time, experts warned this year of the need to regulate the rapidly advancing technology. Geoffrey Hinton, a machine learning pioneer widely called the “Godfather of A.I.,” quit his part-time job with Google in May so that he could speak more freely about his unease regarding A.I.’s future. Experts have raised concerns that A.I. could spread misinformation, manipulate humans and alter the job market if it isn’t controlled. But innovation continues, and it seems likely that researchers will increasingly use A.I. to attempt breakthroughs in many fields. —Carlyn Kranking

NASA retrieves asteroid bits to shine light on Earth’s origins


On September 24, 8.8 ounces of rock and dust collected from an asteroid named Bennu landed in the Utah desert. The astronomical delivery was the result of a more than seven-year NASA mission in which the agency’s OSIRIS-REx probe journeyed 1.2 billion miles to the asteroid to retrieve the sample. The 4.5-billion-year-old Bennu existed before Earth did, so it could hold clues about how our planet formed and which building blocks of life meteorites delivered here long ago.

Initial analysis revealed evidence of water and a high carbon content on Bennu. While the OSIRIS-REx spacecraft is already off to visit another asteroid, researchers on Earth will study the Bennu sample for two years and set aside some of the rock for later examination. And while much of the rock will be analyzed behind closed doors, a 0.3-inch, 0.005-ounce sample is on display at the Smithsonian’s National Museum of Natural History, so you can get a glimpse of an object that is truly far-out. —J.S.

The Titan submersible imploded while searching for a shipwreck

The world watched in June after OceanGate’s Titan submersible went quiet during a dive to the Titanic. The craft and its five passengers descended toward the famous wreck on Sunday, June 18, at 8 a.m., but it lost contact with its base ship, the Polar Prince, around 10:45 a.m. At 5:40 p.m., roughly three hours after the sub was supposed to breach the surface, officials notified the Coast Guard the craft was overdue. Airplanes and a Bahamian research vessel with remote-operated robots helped scour an area twice the size of Connecticut. Numerous television stations and news outlets covered the search as fears mounted that the crew was running out of oxygen. And on Thursday morning, the Coast Guard found debris consistent with a catastrophic implosion of the submersible.

Onboard was Stockton Rush, the CEO and co-founder of OceanGate, who considered himself a maverick and breaker of rules. He had gone forward with that dive and others despite safety concerns. Two former employees had raised issues about the craft’s hull, and more than three dozen experts warned that catastrophic problems could occur due to company’s experimental approach. Though many in the public waited to hear news about the sub after it went missing, experts expected the worst. And while the actual scientific benefits of Titan’s dive were likely minimal, the sub’s tragic end shed a light on the value of the time and effort that goes into scientific exploration of the deep sea. Scientists who dive to the ocean’s depths for serious study go down in crafts that have undergone rigorous testing. Because of that, nearly 50 years had passed since a fatal accident on such a submersible. That all changed with a company that dove despite multiple warnings. —J.S.

Wildfires burned through Canada and Hawaii


Devastating wildfires dominated the news again in 2023. Blazes set a record in Canada, scorching more than 45 million acres by October. The country’s previous annual record, standing since 1989, was less than half that, at 19 million acres burned. As climate change causes higher temperatures, Canada’s fire season has become longer by about two weeks, and larger fires have grown more common. Hundreds of such “megafires,” covering 39 square miles (10,000 hectares) or more, incinerated our northern neighbor this year. Many had massive clouds above them, like those usually seen above volcanoes, that created lightning and high winds. And Canada’s major burns affected others around the world: During June, parts of the United States’ Midwest and Northeast regions registered the globe’s worst air quality, and pollution reached as far as Spain, Britain and Norway.


Canada’s catastrophic fires weren’t alone. On August 8, a devastating blaze swept across the Hawaiian island of Maui and engulfed the city of Lahaina, killing at least 100 people. The death toll is the highest caused by a wildfire in the U.S. in more than a century, and thousands of residents lost their homes. On the islands, some seasons are hotter and drier due to climate change, allowing wildfires to spread at increasing speeds. Climate change is altering many other such areas around the planet, threatening to make what was once considered extreme fire become more and more the norm—J.S.


UFOs break into government discourse and spark conspiracy theories

In 2023, alien conspiracies and UFO speculation riddled social media, but at the same time, some of the stigma around researching unidentified anomalous phenomena, or UAP, began to break down.


For starters, the U.S. Office of the Director of National Intelligence released a report in January that announced more than 350 sightings of UAPs had been logged by the government since March 2021. Nearly half of these were described as “balloon or balloon-like entities”—a subject that took center stage the following month, when the U.S. government shot down what was suspected to be a Chinese high-altitude spy balloon off the coast of South Carolina. The incident demonstrated how identifying UAPs has implications for national security.


Then, at a House of Representatives hearing in July, former U.S. intelligence officer David Grusch alleged in a testimony under oath that the federal government is covering up evidence of crashed vehicles and biological material believed to be of “non-human” origin. In September, alien discourse appeared in legislative chambers once more, when a self-proclaimed UFO expert unveiled what he claimed were the bodies of extraterrestrials in front of Mexico’s Congress. Scientists balked at the suggestion, pointing to several previous alien theories from the speaker that had been debunked. Ultimately, anyone looking for confirmation of aliens on Earth didn’t get it this year—after a 12-month study, NASA released a report on UFOs in September, stating its scientists found “no conclusive evidence” that the mysterious phenomena have an extraterrestrial origin. —C.K.


Orcas break rudders and sink ships in the Strait of Gibraltar

Maybe it’s a form of play. Maybe it’s a passing fad. Or maybe, as internet onlookers from around the world have facetiously suggested, it’s a full-fledged, female-led orca uprising, planned as retribution for humanity’s presence in the high seas. (Scientists aren’t on board with that last one.) Whatever the reason, orcas off the coasts of Portugal and Spain have been ramming into and breaking rudders off ships in the Strait of Gibraltar. Since 2020, more than 500 interactions with contact between orcas and boats have occurred, and four of these incidents—with two this year—resulted in a vessel sinking, most recently in November.


In May, a scientist suggested the curious behavior started after one orca had a negative experience with a boat, and that it spread as juveniles watched her break rudders. This led people to cheer for the orcas on social media. But in an open letter in August, a group of 35 scientists warned against attributing human traits to the animals. Doing so, they wrote, could lead mariners to take aggressive action against the orcas, which belong to a critically endangered population of fewer than 50 individuals. Indeed, some sailors have thrown firecrackers into the water in an attempt to keep orcas away.


Amid all the mystery around the behavior, one thing seems clear—the orcas do not appear to have malicious intentions. “Quite frankly, if they really wanted to take revenge, they would,” biopsychologist Lori Marino told ABC News in July. —C.K.


Covid-19 entered a new phase

Though, to many people, Covid-19 faded into the background this year, the disease remains a problem as the vaccine response has lagged. On May 11, the Biden administration allowed the coronavirus public health emergency to expire, leading the virus to be treated like other respiratory ailments. (Insurance providers were no longer required to provide free Covid-19 tests, and some medicines, such as Paxlovid, were no longer guaranteed to be free.)


A new variant, XBB, became dominant in early 2023, and in September the Food and Drug Administration authorized an XBB booster, which also works for other Omicron variants. But by the end of October, the Department of Health and Human Services said only about 4.5 percent of the population had received the shots, despite the fact that the Centers for Disease Control and Prevention (CDC) recommended the updated dose for everyone six months or older. The reception was lower than the previous year’s booster, which more than 23 million Americans had received after a similar timespan. The lackluster uptake continued a trend of declining response to boosters. As of December, roughly 70 percent of the population had the primary series of the vaccine, while less than 20 percent had received a bivalent booster. While the virus was not spreading at the rate of previous years, as of early December, more than 5,000 people were hospitalized on an average day and more than 1,200 deaths were occurring each week. Much of the population, including people who are over 65, pregnant or immunocompromised, are still vulnerable to the disease.


And some folks continue to deal with the aftereffects of the virus: This June, roughly 6 percent of the population was suffering from long Covid, according to the CDC. And of those, more than one in four experienced significant limitations in their ability to perform normal daily activities. As the disease continues to evolve, the Biden administration says citizens should expect to have a shot available each fall, like the schedule for flu vaccines. But whether people will actually be receptive to that shot remains to be seen, following the decline in this year’s response. —J.S.


A teenage tyrannosaur fossil preserves what young dinosaurs ate

Adult tyrannosaurs—large, bipedal carnivores of the Late Cretaceous—were fearsome predators in the prehistoric landscape. With their bone-crushing bite force, the fully grown dinosaurs could bring down massive plant-eaters. Young tyrannosaurs, on the other hand, might have had more limited pickings with their slender frames, narrow skulls and blade-like teeth. At least, that’s what paleontologists suspected. But they didn’t have proof until this year, when researchers reported a fascinating discovery: a “teenage” tyrannosaur, with its final meals preserved intact.


The astounding fossil of Gorgosaurus, uncovered in 2009 and described in Science Advances in December, provides the first direct evidence of shifts in a tyrannosaur’s diet from adolescence to adulthood. Within the carnivore’s stomach were four legs—two pairs—from small, bird-like dinosaurs called Citipes elegans. Each pair of legs shows different levels of digestion, suggesting they represent the young reptile’s last two meals, consumed hours or days apart. The juvenile tyrannosaur, which was between 5 and 7 years old, likely had to chase down these fast, turkey-sized prey. The findings suggest that young, agile Gorgosaurus survived on bits of baby dinosaurs until they grew big enough to take down titans. —C.K.


2023 becomes the hottest year on record

Worldwide, 2023 started out warmApril and May ranked among the hottest months of their kind in written history. But when summer arrived in the Northern Hemisphere, records fell left and right. Heat waves gripped regions of the United States and Southern Europe. American municipalities set more than 1,000 daily temperature records in June and July, and residents of Phoenix sweltered through an unprecedented 31-day stretch of at least 110 degree Fahrenheit temperatures. Even heat-adapted saguaro cactuses fell over and died. Oceans warmed to levels unparalleled in the nearly 45-year record, with one thermometer in the Florida Keys measuring “hot tub” heat levels at 101.1 degrees Fahrenheit in July.


The life-threatening heat was wide-reaching: On one weekend day in August, more than 111 million Americans in the South and Southwest were under heat warnings. Month after month—first June, then July, August, September, October and November—clocked in as the hottest months of their kind ever documented. With both climate change and the arrival of the heat- and moisture-bringing El Niño
weather pattern, 2023 is now guaranteed to become the hottest year on record. But since, historically, El Niño’s most extreme heat arrives during its second year, some scientists warn that 2024 might be even more chart-topping. —C.K.


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