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 Ask me Anything about Biology or Evolution! (38)

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SlapShot(2608) pic

Ask me Anything about Biology or Evolution!

I don't want this to be so much of a debate as simply a learning forum. A sort of Q & A if you will, where I will be happy to answer any questions you may have in the fields of general Biology, or more specifically, Evolutionary Biology. OR...Evolutionary Psychology, which is what I am going to be doing my Dissertation on. I will try to offer brief and accessible primer answers, and then will back them with links to more thorough and comprehensive scientific articles or videos.

Thanks for your interest. And, as I said, I don;t want to get into a debate on whether or not Evo is true. We have done that in many other debates here, ad nauseum. My Forum here is for the honestly curious; those who enjoy science and Biology. Anybody trolling, especially the Christian fundie types, will be promptly shown the door. I have decided to try and be more of a teacher here on CD, rather than engaging in flame wars against religion.

Let's go!
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2 points

I would like for you to enlighten me on the theory of abiogenesis or perhaps any other credible theories concerning the origin of life. I've been meaning to look into it on my own spare time but I haven't gotten to it, been very busy with school. Thanks.

2 points

Hey Art, good to see ya. Thanks for the Question.

I knew it wouldn't be long before somebody asked this one. Since it is one of the very few aspects of Evolution that we don't have a solid, irrefutable answer for just yet. It is sort of the biological equivalent of the Big Bang theory in Cosmology. Cosmologists and Astroiphysicists can tell us what happened and how the Universe expanded and came to be in its present state. And they can nail it down to what occureed at 10^-43rd of a second.

That number looks like this: 0.000000000000000000000000000000000000000043.

Wow! So, like a trillionth of a trillionth AFTER the Big Bang, we can give a blow by blow account, how plasma cooled enough to form the first atoms and molecules, and all that. But we don't know what CAUSED the BB to happen. Or what came before.

So it is with Evolution. The Origin of Life. Abiogenesis. The word meaning "genesis" or creation without life (Bio). A-bio. Life from non life.

So our current theory thinks life here on Earth began on a microbial level, in the warm primordial ooze, about 3.5 BYA. Since the Earth is about 4.6 BYO, we're looking at a full 1 Billion years for those first single-celled microbes to appear.

What needed to happen was for amino acids to from proteins, and in turn for those proteins to form rNA and then DNA. (this idea that rNA might have come first is relatively new, as for a long time we thought DNA was the pre-cursor.)

But now we think it was most likely rNA. That is, messenger DNA. Or "re-combinant" DNA. It is sort of like the chicken and egg riddle. Which came first? The rNA is the type of DNA (de-oxy ribonucleic Acid) that forms the templates when the DNA splits and carries the necessary info and codes for the molecule to replicate, that is, make more copies of itself.

But how does all this happen? Can we replicate those earthly conditions from 3.5 BYA? And see if it's possible to "grow life" from an inorganic warm soup? (Some like to call that "Darwin's Warm little pond."

We tried, and the last time we did we cam very close, We created proteins! From nothing. But not DNA. Yet.

Tnhe first attempt was back in the 1950s--, these ideas were put to test by Stanley Miller and Harold Urey; they conducted the famous Miller-Urey experiment, which would be replicated multiple times under more representative conditions. That was the start of an experimental approach to the origin of life!

Nowadays, we're trying to figure out how and where genetic material and proteins were synthesized. Some pathways are already described, although the big picture remains uncertain. The search goes on in three main trends: the RNA World ('genes first'), the metabolism-first models and the surface hypotheses

It was proposed at least two times that RNA was a likely candidate to look out for, because RNA could carry information like DNA and carry out biochemistry the way proteins do. This idea, called the "RNA World", can thus be summarized as follows:

“RNAs were the original biological catalysts in pre-cellular times - the so-called RNA world.”

We are now looking for biochemical reactors, where RNA could have been constructed. Hydrothermal vents (chimneys at the oceans floor) are proposed to be RNA-making reactors where PCR-like reactions could occur---in other words, a 'vessel' where the amount of a certain bio-molecule could be amplified. It must also be noted that they possess an H+ (positive hydorgen ion) gradient, which can be used as an energy source. In summary, these vents are possible locations for the replication of genetic material and the synthesis of its precursors. Now we must focus on the question how RNA and proteins were formed.

Personally--this is MY favorite theory. The super-heated undersea hydrothermal vents would be ideal "wombs" to get this whole process kick-started. We have in the last decade or so seen that life can occur under the oceans in places and conditions we had previously thought impossible. We're talking without oxygen (anaerobic!) and in water temps of near boiling (212 degrees F).

RNA could have been synthesized from pyrimidine ribonucleotides (T, U, C), which in turn are synthesized by simpler precursors (this solves the issue with cytosine; namely that is broken down faster than it is made). Yet, RNA is a very unstable molecule, so other researchers have proposed RNA-like precursors: simpler molecules that mimic RNA. Examples are Peptide)NA, T(hreofuranosyl)NA and G(lycol)NA. PNA has gained attention because it bonds with DNA, has biological significance in current cells and its precursor is detected in microorganisms.

The RNA-World could then be pushed aside by the appearance of DNA (in primitive lipid cells that were much simpler and smaller).

How this transition occurred, is not yet known, although it has been proposed that VIRUSES might have played a role in this.

BUT...There are some in my field stating that RNA could NOT have been the first molecule, because chemistry has failed to produce RNA under laboratory conditions (remember the struggle of organic chemistry). Moreover, new evidence has indicated that amino acids are also likely candidates for the first molecule, instead of RNA. Amino acids are much more stable and easier to form under prebiotic conditions.

Here's a nice little primer video, only about six minutes long..........

1 point

Wow, very interesting theory, thanks for taking the time to answer. Hopefully they will find a solution to this RNA versus DNA dilemma. Also, is the approximate time for which the RNA or DNA might be synthesized known at all? I mean if the process of protein synthesis is relatively quick, why not, then, conduct multiple, rapid experiments, each with its own manipulated variables which accommodate the varying theoretical conditions. Sorry if this is a stupid question in advance.

1 point

Other than Abiogenesis, I forgot to mention there is another theory as to the origin of our life here on Earth.

Years ago when I first heard of it, when I was an undergrad, I initially found it fairly preposterous. But as time went on and I learned more, both about how much we DON'T know about the exact mechanics of Abiogenesis, as well as how vast the Universe is and how it most likely teeming with life, I began to lend some possibility to the notion.

And, pray tell, what IS this 2nd notion of life origin?

Panspermia, baby.


Let me know if you would like to discuss.


arteaga34(130) Clarified
1 point

Seems like a very much more interesting theory that's for sure! I suppose it's perfectly plausible if the big bang is true, though. We should blast some bacteria or germs to some earth-like planet thousands of light years away from us and see what happens.

1 point

My question is if context is ulterior to value, is there something that's then beyond context? Is logic the means of evolution, and if so, is logic unto itself, or is there say a property or force that itself informs the existence of logic?

1 point

The word "logic" is a man-made unit of speech. Which is of course what words are.

Nature itself, and Evolution, the process of it, do not "think." Nature is neither logical or illogical. It "acts." It "reacts." It adapts. Or it doesn't, and thus perishes.

Evolution itself is based on totally random genetic mutations. And if those mutations cause for the host organism to develop some sort of physiological trait that is advantageous in its given environment, then that mutation and trait will be passed on to progeny. Who will thrive. Dominate. And finally prevail and be of the only type of that species that is left; the one that was lucky enough to inherit that initially random genetic mutation.

What was once a rare aberration, becomes the new norm. This is selective inheritance.

It does not think. Logic is a misnomer. The word does not fit into this paradigm. It's apples and oranges.

So your post is best left to a philosopher and not a biologist such as myself.

>>>>>I should add here that, although I personally do not believe in this, a very FEW Evolutionary Biologists DO believe that the Evolutionary Process is DRIVEN by a sort of Universal Intelligence. A Divine Creative Force. I will not use the term "god" here. As even these believers--considered pretty radical by most of us--only are postulating the existence of a DEIST type entity. That is, a non-caring,non-personal sort of god. More, really, or a Universal Life Force than a biblical god.

These folks believe then, that those initial genetic mutations are not random at all, but are instilled, created, by this Life Force. Call it what you will: Universal Mind, maybe?

This school of Evolution is called "Teleological" Evolution. Meaning that it is driven and has a pre-planned purpose.

Again I add, believers of this comprise the vast minority of us.


I believe that the Big Bang occurred to a reoccurring cycle of collapsing and expanding of the universe. The energy that is created when that occurred allowed the Big Bang to occur sometime after. It will happen again sometime into our future.

1 point

Thank you very much. I too subscribe to the general notion of a universal force.

1 point

When is the human organism's genetic code formed? Fertilization? Implantation?

1 point cats are asking some pretty damn good questions. Thank you.

OK, I'm not sure how much you already know about DNA so no offense if I begin by telling you some stuff you already know...........

DNA, or deoxyribonucleic acid, is genetic material that exists in nearly all living organisms, including humans. Any organism with nucleus-based cells has DNA. It is the building blocks forming an organism, and the DNA combination an organism is born with remains the same.

So, we now gotta get a little more complex.

There are FOUR types of DNA: mtDNA, rDNA, nDNA, and recombinant DNA. DNA is a double helix in which genes result from base pair combinations. It has the ability to replicate itself. Human DNA has 3 BILLION base pairs formulated using four chemical bases: adenine (A), cytosine (C), guanine (G), and thymine (T). It is kept in a cell called a chromosome.

The "chromosome" is what undergoes a splitting process to recombine and form new cells. Offspring of an organism contains DNA from both parents.

(nDNA or nuclear DNA, forms in the nucleus of an organism’s cell--which, come to think of it, might be the ONE thing you were most curious about in your Question? That is, where it all started?)

The cell ALSO contains a cell membrane called the mitochondria. This is often called the "power-house" or the "engine" of the cell. A small amount of DNA referred to as mtDNA is found in the mitochondria rather than the nucleus. (rDNA or ribosomal DNA helps create proteins the body uses to generate cells.)

rDNA becomes mRNA, which is the protein formation. rDNA can also mean recombinant DNA. (NOTE.....This DNA is designed solely in laboratories for cloning or creating genetic sequences that would not exist otherwise.


Here's a nice, short little video that lays this out pretty well.......

Very true at that as well, but if I'm correct, we are only half way done with the life cycle of the universe. A lot can happen in that time period. But hell, we won't be here to see it (the sun will engulf earth wayyyyyyyyyyyyyyyyyy (like billions/trillions of years) before that happens).

Yeah, what's up with the Fibonacci number?

1 point

I LOVE Fibonacci's number.

Actually that is sort of a misnomer, since what we see in Nature that's called Fibonacci's "Number" is really Fibonacci's 'ratio of numbers." More of a geometric pattern than a number.

It is easy to learn the scale by heart, you just start with "1" and then as you go, the next number in the sequence is the sum of the two numbers before it.

So.....1,1, 2, 3, 5, 8, 13, 21, 34, 55, 89, etcetera....

We find it in many places in nature. Pine cones; Nautilus shells; flowers; honeycombs form bees; spiderwebs.

I think it is one of the signs that there could be some sort of underlying Fabric of Intelligence in Nature. A sort of Driving Force. (No, NOT a god!) LOL.

That reminds me of Rupert Sheldrake and his ideas on a thing called Morphic Resonance. Which basically posits that Nature has a sort of Mind, that can learn and remember, as well as teach.

But I am straying off topic. Thanks for bringing up Fibo, Cap Con. Another mathematically-based pattern, or geometric aspect we find in nature is called the Golden Mean. It is usually seen in Art, as it is the ideal proportion of a rectangle. the short sides to the long sides. I think it is 1.62.

Here is a pretty cool video on this stuff. Nice visuals! Nothing beats the Beauty of Nature. It is exultant. And is my God.

Ah okay thanks for explaining :D

1 point

When did Radical Islamist evolve ? How far back does that evolution go ?

SlapShot(2608) Disputed
1 point

This is a history or religion question. NOT Science.

And since I am pretty sure you did it on purpose,I'm gonna go ahead and take that as a troll.

So, as I said in my opening rules...adios asshole.


1 point

Could you say something about evolutionary theory that we can't find out from attending a high school biology close or googling? Thanks JC.

SlapShot(2608) Disputed
1 point

Sure...whatever you want. Ask me a question, as the topic is far too broad and complex to just guess at some detail of Evolution you want to know about.

Would you like to talk about the Theist's or the IDer's favorite argument against Evolution? Which is what they call "Irreducible Complexity?" And perhaps an example of what they think shows that? And us Atheist Evolutionary Biologists can effectively debunk that theory? Or if you don't believe in Evolution, give me an example of why not. And then I will debunk that as well.

Let me know.

Atrag(5550) Clarified
1 point

What do you consider the most significant research in evolutionary biology in thr last year and to what extent does it differ to Darwins original theory?

SlapShot(2608) Disputed
1 point

I doubt I COULD tell you anything you could not Google.

But, what is a biology "close?" As a Biologist I am interested, as I am not familiar with that term.

Atrag(5550) Clarified
1 point

I meant course. If you were studying for a PhD in evolutionary biology you would be able to tell us something that isn't easily understood from a google search.

I take it you can't answer my question then?

How about the evolution of biology itself from the Dark Ages when the Church ruled through the Age of Enlightenment / Renaissance Period to the present day. The Church had a chilling effect on science and discovery when it ruled with an iron fist and as its hold weakened science and arts exploded. How did biology benefit from this?

2 points

Religion has never been a friend to science. Except for the odd fact that back in the day, a men of religion also happened to dabble in science. During the era of the Holy Roman Empire, they had all the $$ so they could afford to fund their research.

Except woe betide the clergy man who made some sort of discovery or observation that flew in the face of Church dogma. If this happened they were silenced, or forced to recant by threat of discontinued funding, or worse. Like death. Or at least house arrest (as with Galileo) or other sanctions.

Here is a brief timeline on significant achievements and discoveries in the field of Biology from the times you mentioned in your OP..........

Leonardo's anatomical drawings: 1489-1515

In about 1489 Leonardo da Vinci begins a series of anatomical drawings. For accuracy of observation they are far in advance of anything previously attempted. Over the next twenty-five years he dissects about thirty human corpses, many of them at a mortuary in Rome - until in 1515 the pope, Leo X, orders him to stop.

His drawings, amounting to some 750, include studies of bone structures, muscles, internal organs, the brain and even the position of the foetus in the womb. His studies of the heart suggest that he was on the verge of discovering the concept of the circulation of the blood.

Illustrated books: 16th century

It is a coincidence of great value to biology, in which observation is of prime importance, that the Renaissance revival of interest in science coincides with the invention of printing. As soon as books can be published with woodcut illustrations set among printed text, naturalists have not only a large new readership but also the ability to show what they have so carefully observed.

The first to make serious use of this opportunity is a botanist, Otto Brunfels, whose three-volume Herbarum vivae eicones (Living images of plants) is published in Strasbourg between 1530 and 1540.

Brunfels' pioneering example is soon improved upon by another German botanist, Leonhard Fuchs, whose Historia Stirpium (History of plants) is published in Basel in 1542. Fuchs introduces a new accuracy, in his depiction and his verbal description of the plants.

A French naturalist of this period provides a good example of the Renaissance impulse to match and perhaps even outdo the classical authors. In 1546 Pierre Belon sets off on a two-year tour of lands round the eastern Mediterranean with the specific purpose of finding and depicting animals and plants described by ancient writers.

Belon's travels and observations are recounted in a succession of illustrated volumes published in Paris during the 1550s - on fishes and dolphins (1551), on conifers (1553), on general Middle Eastern curiosities (1555), on birds (1555) and finally 'portraits of birds, animals, snakes, herbs, trees, men and women of Arabia and Egypt, together with a map of Mount Athos and of Mount Sinai for the better understanding of their religion' (1557).

Belon is an unashamed generalist. Meanwhile a highly specialized volume, the most significant of all the early illustrated scientific works, has been published in Basel in 1543 - bringing to a wide public the discoveries of Vesalius.

Vesalius and the science of anatomy: 1533-1543

A young medical student, born in Brussels and known to history as Vesalius, attends anatomy lectures in the university of Paris. The lecturer explains human anatomy, as revealed by Galen more than 1000 years earlier, while an assistant points to the equivalent details in a dissected corpse. Often the assistant cannot find the organ as described, but invariably the corpse rather than Galen is held to be in error.

Vesalius decides that he will dissect corpses himself and trust to the evidence of what he finds. His approach is highly controversial. But his evident skill leads to his appointment in 1537 as professor of surgery and anatomy at the university of Padua.

In 1540 Vesalius gives a public demonstration of the inaccuracies of Galen's anatomical theories, which are still the orthodoxy of the medical profession.

Galen did many of his experiments on apes. Vesalius now has on display - for comparison - the skeletons of a human being and of an ape.

Vesalius is able to show that in many cases Galen's observations are indeed correct for the ape, but bear little relation to the man. Clearly what is needed is a new account of human anatomy.

Vesalius sets himself the task of providing it, illustrated in a series of dissections and drawings. He has at his disposal a method, relatively new in Europe, of ensuring accurate distribution of an image in printed form - the art of the woodcut. His studies inaugurate the modern science of anatomy.

At Basel, in Switzerland, Vesalius publishes in 1543 his great work - De humani corporis fabrica (The Structure of the Human Body). There are seven volumes including numerous magnificent woodcut illustrations. The book is an immediate success, though naturally it enrages the traditionalists who follow Galen. Galen's theories have, after all, the clear merit of seniority. They are by now some 1400 years old.

But for those willing to look with clear eyes, the plates in Vesalius's volumes are a revelation. For the first time human beings can peer beneath their own skins, in these strikingly clear images of what lies hidden.

Attempts at classification: 1583-1704

It is a natural impulse for any academic, confronted by the bewildering array of nature's living forms, to try and establish some degree of order. One of the first to make a successful attempt is Andrea Cesalpino, whose De Plantis of 1583 classifies plants according to the characteristics of their flowers, seeds and fruits.

The Swiss physician and botanist Gaspard Bauhin extends Cesalpino's work in two books (Phytopinax 1596, Pinax theatri botanici 1623). Both titles mean 'gallery of plants', and Bauhin classifies some 6000 examples. The main significance of his work is that he is the first to arrange plants in separate groups, or genera.

Bauhin's work was the beginning of the binomial (two-name) system which subsequently prevailed in the classification of living organisms. Each is placed in a category, and the classification combines the name of the category with that of the wider group of which the organism is considered to be a member..

These two levels of classification eventually become standardized as the genus and the species. A basic problem of classification within this arrangement is to decide how much apparent variation can be allowed to plants or animals grouped as a single species. This is resolved in the work of the English naturalist John Ray, who makes extensive tours in Europe during the 1660s with his patron Francis Willughby. Their express purpose is to classify all plants and animals.

Ray publishes classifications of birds (1676), plants (from 1682), fishes (1686), land animals (1693) and insects (1705). In their original partnership the plan was for Willughby to undertake the animals and Ray the plants. Willughby dies young, in 1672, and Ray credits him with the text on birds and fishes (though amplifying it himself).

The greatest achievement is Ray's own work on botany. The Historia Plantarum (1686-1704) describes some 18,600 plants, categorizing them in ways which hold good today. His most influential decision is defining a species as a group which has a mutual fertility, each member capable of reproducing with any other. Ray's efforts prepare the way for Linnaeus.

Harvey and the circulation of the blood: 1628

A book is published in 1628 which provides one of the greatest breakthroughs in the understanding of the human body - indeed perhaps the greatest until the discovery of the structure of DNA in the 20th century.

The book consists of just fifty-two tightly argued pages. Its text is in Latin. Its title is Exercitatio anatomica de motu cordis et sanguinis in animalibus ('The Anatomical Function of the Movement of the Heart and the Blood in Animals'). Its author is William Harvey. In this book he demonstrates beyond any reasonable doubt an entirely new concept. Blood, he shows, does not drift in the body in any sort of random ebb and flow. Instead it is pumped endlessly round a very precise circuit.

Until now it has been assumed that the blood in arteries and the blood in veins are different in kind. It is well known that they are of a different colour, and there have been many theories as to what each supply of blood does.

The most commonly held belief is that arterial blood carries some sort of energy connected with air to the body (not far from the truth), and that blood in the veins distributes food from the liver (less accurate).

By a long series of dissections (from dogs and pigs down to slugs and oysters), and by a process of logical argument, Harvey is able to prove that the body contains only a single supply of blood; and that the heart is a muscle pumping it round a circuit.

This circuit, as he can demonstrate, brings the blood up from the veins into the right ventricle of the heart; sends it from there through the lungs to the left ventricle of the heart; and then distributes it through the arteries back to the various regions of the body.

After much initial opposition, Harvey's argument eventually convinces most of his contemporaries. But there are two missing ingredients. His theory implies that there must be a network of tiny blood vessels bringing the blood from the arterial system to the venous system and completing the circuit. But his dissections are not adequate to demonstrate this. It is not till four years after his death that Marcello Malpighi observes the capillaries.

And Harvey is unable to explain why the heart should circulate the blood. That explanation will have to await the discovery of oxygen.

Malpighi and the microscope: 1661

Marcello Malpighi, a lecturer in theoretical medicine at the university of Bologna, has been pioneering the use of the microscope in biology.

One evening in 1661, on a hill near Bologna, he uses the setting sun as his light source, shining it into his lens through a thin prepared section of a frog's lung. In the enlarged image it is clear that the blood is all contained within little tubes.

Malpighi thus becomes the first scientist to observe the capillaries, the tiny blood vessels in which blood circulates through flesh . They are so fine, and so numerous, that each of our bodies contains more than 100,000 kilometres of these microscopic ducts.

With their discovery, the missing link in Harvey's circulation of the blood has been found. For the capillaries are literally the link through which oxygen-rich blood from the arteries first delivers its energy to the cells of the body and then finds its way back to the veins to be returned to the heart.

Leeuwenhoek and the microscope: 1674-1683

Malpighi's pioneering work with the microscope is taken further by the Dutch researcher Anton van Leeuwenhoek. Teaching himself to grind lenses to a very high degree of accuracy and clarity (some of them providing a magnification of 300x), he uses a simple microscope with a single lens - in effect a tiny and extremely powerful magnifying glass.

With instruments of this kind he is able to observe phenomena previously too small to be seen. In 1674 he is the first scientist to give an accurate description of red blood corpuscles. In 1677 he observes and depicts spermatozoa in the semen of a dog. In 1683 he provides a drawing of animalculae (or bacteria) seen in saliva and dental plaque.

His discoveries, published for the most part in the Philosophical Transactions of the Royal Society in London (though he himself lives in Delft), vividly suggest the excitement of being the first to wander with such enlarged vision among the minutiae of the animal kingdom.

His account of the common flea follows its development from egg to the practical perfection of its adult anatomy. His researches demonstrate for the first time that the tiniest living things have a life cycle and generative systems like any larger creature.

All I can say is WOW, what a response. I wasn't expecting anything like this. What a great history lesson for any and all. Thanks for replying.

1 point

There is an awful lot of faith in far reaching abilities thought capable in biology. Evolution purposes to assembe mutations for purpose of progress, and to further adaptation.

Evolution without a Creator is only selective of biological attractions based on these three basic needs to sustain durability, for survival and to further evolve toward progress through adaptations. But biology has no selection ability for preference!!

This kind of faith in evolution's ability absent a Creator is fairy dust!

It's a heavy acid trip to think evolution without a Creator can manage its designs selective also of preference, attracting mutations that will lead ultimately to design and artistic beauty too. It would actually look like crowded desolate waste with creatures durable and more likely ugly.

Thinking biology can evolve to select mostly beauty is unrealistic!

There are not enough care Bears and fairy dust to sustain that dream!

I'm sure organized artistic beauty can evolved through preferred biological selections for beauty in your make believe word of evolution But really... That's pretty neive faith in evolution's biological focus and creative abilities!

0 points

LOL, what an arrogant bigot. You are going to teach other's how to also be bigots? You don't even posses the simple intelligence & compassion to respect all people's beliefs. You actually think you have the answers to life? What a fool, you would make the perfect bigoted Liberal biased professor in so many Colleges today.

Atrag(5550) Disputed
6 points

The amount of fear in your post is amazing.

FromWithin(8239) Disputed Banned
2 points

Try addressing the amount of narcissism in his argument and many posts.

1 point

FromWithin's post?

Yeah, I know. He pretty much runs scared around here all the time. Especially when my science threatens his religious beliefs. LOL

SlapShot(2608) Disputed
1 point

I figured you would be stupid enough to break my rule here on MY science forum.

So you're banned.

Adios, asshole.

Too bad for you, you might have learned something.