The Very First Animal Appeared Amid an Explosion of DNA
nytimes.com
nytimes.com
Um. If this gene was the result of a mutation, isn't it possible, at least in theory, that mutation happened more than once? At two different times? At two different branches on the species tree?
Not really my area but there seems to be an assumption that species development (dare I say evolution) was linear, with humans being the ultimate achievement in that process. But doesn't the fact that genes mutate - sometimes triggered by viruses - imply the process was not at all linear?
I think it is also true to say that convergent evolution often produces results that differ genetically, even though the resulting phenotypes serve the same purpose.
It's speculated those regions are gene foundries, but it's mostly speculation with limited evidence.
In zebrafish and mouse, the more "developmental" a gene is, the more SPACE it seems to have around it. More space means more regulation and more potential for new regulation.
The relative lack of non coding DNA in other, simpler cells doesn't tell us that we don't need ours. It's equally possible that our DNA is just making significantly more dynamic decisions.
And it's not necessarily that they have more coding regions. It's that they have a greater percentage vs noncoding. It's a proportional thing.
Genes are long sequences of information. You could easily have quite different genes doing similar things, but if you have the very same gene (sans minor differences) it's just too unlikely to have originated completely independently twice.
The closest thing I can imagine to your scenario is where, because of shared ancestry, 2 species have a certain gene, and then some minor mutation hits both of them, and now they both have some other gene. I suppose that's possible. But they already shared the original gene to start with.
As an example, write a simple program that randomly generates strings of letters from 1 to 20 characters in length. Then include an English dictionary in the program. Compare the randomly generated strings with the words in the dictionary. How often does the random process generate actual words? Not often, but sometimes, and that is all that is needed.
Your example totally ignores how selection works. Life does not generate genes randomly and see what sticks. Prebiotic chemistry might have worked like that to some degree. But at the point oxygen transport was invented every gene in an organism would already been subjected to billions of years of selection pressure and the gene or genes that eventually came to code for hemoglobin would already have had some other, related purpose.
What do you think the word "selection" means? It means that stuff dies. It means that there is constant random mutation, most of which leads to death. Of the mutations that are useful, we say they are selected. When we speak of a gene being selected, we should recall that many mutations are failed mutations that lead to death. It is a random process. If you think there is some guiding force that leads genes down the correct path, then you are basically making a religious argument.
"isn't it possible, at least in theory, that mutation happened more than once?"
The answer is obviously "yes". Even taking your own words, the answer is clearly "yes", so I'm not clear why you are arguing. Even in the extreme case, where mutations lead to death 99.9999% of the time, the answer would remain "yes". Your own math shows the answer is "yes". I'm sure you know what convergent evolution is:
http://www.zo.utexas.edu/courses/thoc/convergence.html
As it says there:
"Molecules can evolve convergently"
I think you wanted to make the point that this is rare. You should have said so. You could have answered gort by saying "Yes, but this is rare." Instead, you've taken an indefensible position.
In other words, if you need to hit haemoglobin exactly, odds are absurdly against that. But if there are 1e30 different genes resulting in substances that all increase oxygen saturation of blood, that then "coalesce" on haemoglobin as a result of optimization. In other words, I'm asking "haemoglobin" (and variants) are the bottom of a valley of an optimization process. But for evolution to "find" haemoglobin, it doesn't need to hit the bottom, it only needs to hit the valley. So it matters a great deal how big the valley is, and such a valley can be quite big. And I get it: we have no hope in hell of figuring out how big the valley is, so we just take this as answer.
So "What good is half a wing ?". Well if 1/1e30th of a correct gene already works, then "half a wing" can be quite bad and yet result in a wing. DNA is an optimization process, and if that was the defining change being selected against, is it that hard to imagine that it would converge on haemoglobin given 1e30 starting positions.
If you look at online evolution simulators, the ones with the wheel racing [1], then the "spikes for and aft, small wheel forward, big wheel aft, with a tail spike to prevent tipping over" could be haemoglobin in this example. The valley surrounding that optimal outcome is huge : it's essentially the whole universe in that case, which is a "gene" with 14 float32's and 2 integers. How many combinations is that ? Quadrillions, at least. And yet, all roads lead to Rome, or at least to the tailed bigwheel.
Of course this doesn't even seem to apply to haemoglobin. Haemoglobin and chlorophyll[2] aren't that different (in fact the gene is identical, or at least there are genes that code for chlorophyll and genes that code for haemoglobin that are identical, so ignoring variations, they're actually identical. The difference is not so much in the gene itself but what happens to the molecule after it's created, it's in the "meta" information in the gene, not in the transcription part). So what really needed to happen is a screwup in the haemoglobin gene animals inherited from plants, followed by a few hundred generation of fine tuning. (in fact, that molecule does other stuff too, animal blood, plant photosynthesis, and (most) plant colors, as well as some aspects ATP generation (and I'm sure there's more, we just haven't found those functions yet) have a very similar chemical basis, and therefore are likely regulated by very similar genes).
That could have happened 1000 times. Easily.
[1] http://rednuht.org/genetic_cars_2/
[2] https://patch.com/georgia/cascade/bp--hemoglobin-vs-chloroph...
Unlikely, but not absolutely impossible. Correct?
Editorial: This is where Science / science loses me. It makes absolute statements that aren't in fact truly absolute.
The point being, __if__ there was a chance identical mutation that changes (a lot?) of things. Truth be told, life coming into being has to be a couple orders of magnitude coincidental than some gene mutation. In that context, "too unlikely" starts to feel much less so, yes?
The only thing this encourages is crap like creationism and flat earth theory because there is no way science is ACTUALLY SURE.
Correct but irrelevant. Winning the Powerball 100 times in a row is also not absolutely impossible. Nonetheless, it won't happen.
Think about winning the spermatozoan race 2 millions of times in a row, as member of the most intelligent species known in the universe, one among millions of different forms of life, after surviving five consecutive massive extinctions that wipped the 90% of the life in the planet each time.
Statistically speaking, we can't be real.
The occurance of something is also a function of the total universe of occurrences. This doesn't seem to be part of the "close to impossible" numbers being mentioned.
If life itself was the result of a roll of the cosmic dice then anything down stream sounds reasonable.
That matters here because we're not talking about any single cell or single strand of DNA. We're talking about millions upon gazillion. So "the game" is being played an unimaginable number of times. Clearly that changes the possibility of an outcome.
Actually, it's quite imaginable. Not only is it imaginable, it's fairly straightforward to calculate an upper bound on the actual number, and from there to calculate the odds of producing the same gene completely independently more than once. If you do the math you will find that the odds are indistinguishable from zero.
Science doesn't (intentionally) forget about unlikely alternatives. That doesn't mean there is any good reason to treat highly unlikely scenarios as the equals of the vastly more likely cases.
And arguing anything about chances based on things that have already happened is kind of bullshit. They already happened, however unlikely. We know unlikely things can and do happen occasionally. That does not mean other unlikely things are more likely to happen.
And if you really insist on doing that, keep in mind the timespans here also differ by orders of magnitude.
Only amongst people who haven't done any reading or learning about evolution.
> the process was not at all linear
Indeed.
> If this gene was the result of a mutation, isn't it possible, at least in theory, that mutation happened more than once?
Yes. But if the gene is nearly identical in sharks as in humans, the chance of that happening from convergent evolution would be small enough that "they have a common ancestor" is a much more likely cause.
It is definitely possible that the two same mutations for hemoglobin happened at different points in time, but as I understand it, there is an assumption of parsimony. In other words, it is much more likely that the creation of genes for hemoglobin for sharks and humans happened at the same time than at different times.
I think we will always have a special place in the history books (perhaps not a pleasant one) because we were the first to have some ability to consciously edit not only our DNA but the DNA of other species.
Thinking about it, if life begin in millions of different universes, there would seem to be one of two possible outcomes. Life eventually goes extinct (due to something happening on the planet that life can't evolve to survive, if nothing else the death of the planet's star), or life develops a species with enough intelligence to be able to modify their own evolution. An idea similar to the anthropic principal. Though different in that we are a sufficient end case for the anthropic principal, but we haven't reached a sufficient end case in regards to evolution (though we have begun to grasp it).
It's unlikely that the sequences of the two independently evolved proteins would be so similar; you also wouldn't see a chain of progressively similar hemoglobins as you moved down the gene tree to older ancestral organisms.
Not anymore - though it depends on what precisely you mean by convergence, of course. I highly recommend the new book Improbable Destinies by Jonathan Losos[0]
[0]https://www.amazon.com/Improbable-Destinies-Chance-Future-Ev...
This was argued out a while ago with stick insects that lost and then regained the ability to fly (several independent subspecies did this). A lot of people thought it meant the stick insects "completely lost all the genes associated with wing formation" and then "gained an entirely new set of genes that caused wing formation", but folks in the evo devo world believe- and I agree- that the insect never lost anything except a few regulatory domains that managed the expression of pre-existing components that are depended upon by multiple other subsystems (IE, wings are composed of basis proteins that are used for many body parts).
My interest is in molecular evolution, not full character traits, because those phenotypes are incredibly complex and IMHO beyond our current level of sophistication in analysis.
I'm no expert and could be wrong but I think this is what Losos is referring to in his book. For example, "New and Old World porcupines do not share a common evolutionary heritage… The two lineages have independently evolved their quills from different, unquilled rodent species." Dozens of stuff like this. He goes into more detail with tropical island anoles, his field of expertise, and orients the whole discussion around Stephen Jay Gould and Simon Conway Morris's competing views on the overall paradigm of convergence.
See this NPR interview for a quick summary[0]. A key quote (which I'm not discerning enough to tell if it challenges your claims or if your claims are actually already in response to these claims): "the flood of molecular DNA data that has come forth in the last two decades or so has in many cases revised our understanding about how species are related to each other. And it has revealed that many species that we thought were similar because they're closely related, that they're not closely related and that their similarity is the result of convergent evolution."
https://www.npr.org/2017/09/07/549250035/biologist-jonathan-...
There's nothing surprising or interesting about that- spike shapes are common in nature and probably fall out of basic genetic evo-devo rules naturally.
Not if you're a mossy frog -
http://fuckyeahconvergentevolution.tumblr.com/post/839362577...
However, in the case of hemoglobin this is unlikely because this gene is particularly large, and sensitive to change. As a result it is highly "conserved". That is, mutations in this gene are selected against at a high rate because they tend to be deleterious.
To create a gene like hemoglobin, you'd need hundreds of mutations to develop a hemaglobin gene from raw material. It is possible, but unlikely that humans and sharks would have independently accrued the same exact mutations in the same places since their divergence to create the same gene. It is far more likely that since this gene is essential, it has remained mostly unchanged since the divergence of sharks/humans from their common ancestor.
https://www.sciencemag.org/news/2013/09/bats-and-dolphins-ev...
Some genes appear very early in the tree of life. Others have re-evolved two, three, or hundreds of times. This happens both because there may only be one reasonable way to encode the same function or because the same existing structure can be re-used for the same “new” function (evolution often re-uses existing features because that’s far easier then evolving ex nil)
Let me reassure you that computational biologists who do these kinds of analysis are very aware that evolution is not linear (hence the many methods for building evolutionary trees), and that similar mutations could (and do) occur in different branches of a tree. The argument being made here is that something new has appeared -- there are many new trees that emerged about 650 million years ago. (In the protein world, 650 million years is a relatively short time, so evolutionary relationships at that distance should be detected.)
That said, it is very dangerous to talk about "novel genes" or "novel proteins" without being very clear about the nature of the novelty. Just as protein sequence comparison is more sensitive (has a longer evolutionary look-back time) than DNA sequence comparison, there are methods (not used in this paper) that can look back even farther, and we know that there are ancient evolutionary relationships that are difficult to recognize using sequence comparison, the approach used here. Moreover, many proteins are build from modules (called domains) that can be rearranged, so even though the module might be old, the particular arrangement might be newer. After a quick scan of the paper, it was unclear to me whether the authors are claiming that there are a large number of genuinely novel domains (unlikely), or simply arrangements (more likely), or perhaps simply duplications of existing genes (very likely, but not very novel).
So, basically, the total number of sharks having been born and having reproduced. It must be large, but probably not enough to beat the odds.
Or that some DNA capture happened in some part of the road. Now we have transgenic tomatoes with flatfish genes in their DNA. There is not any guarantee that the common ancestor of both species would had developped those genes yet at the time of the code fork.
AFAIK, genes contain base pairs, and a base pair encodes 2 bits of information (computer engineering perspective here ;))
When they say 55% is the same, do they mean: 55% of genes have a similar structure and amount of basepairs, or do they mean: exact same values for the base pairs bit for bit?
Like for example gene rs4778138 has an effect on eye color (handwavy first search result of snpedia for the example here). So if in two humans, this rs4778138 has a different value, do they consider both humans to have the same gene (because it is one that encodes eye color to some value in each case), or a different gene (because it encodes a different eye color)?
If you say that 55% of the genes in the human genome were already present in the first animal, then you're saying that stretches of DNA which bear a significant similarity to 55% of ours were found in the first animal.
Not just copying DNA, but also a cell wall and nucleus etc. On top of that multi cellular organisms are on the evolutionary slow lane, they have smaller populations, take longer to reproduce, and don't simply hot patch any random bit of DNA they come across.
What they've done is assigned A/T/C/G to North/South/West/East and ended up with that walk plot. They go into some detail on the overview page about the significance of the plot, but overall point is that "DNA Walk makes patterns in the genomes sequences apparent. Clustering of repeats, palindromes, horizontally transferred genes, telomeres, and GC skew can be easily spotted using this visualization approach."
Interactive E. Coli link can be seen at http://www.g-language.org/g3/ (click on the DNA Walk tab view).
Metazoa (760mya) - "animal multicellularity (gene regulation, signalling, cell adhesion, and cell cycle)"
Eumetazoa (760-680mya) - "Characteristics of eumetazoans include true tissues organized into germ layers, the presence of neurons, and an embryo that goes through a gastrula stage." [1]
Planulozoa (680mya) - "A 2004 study investigated the relationships between biradial and bilateral animals in evolution. If biradial is the link between radial and bilateral, then would seem to suggest that bilateralism occurred before cephalization. Called the Planulozoa Hypothesis, the authors suggests that ctenophora are the sister clade of bilateralians, and that all three of the groups – cnidarians, ctenophora and bilaterals – are the descendents of a single bilateral ancestor." [2,3]
Bilateria (650mya) - "A Hox system is thought to have arisen (indicated by a red bar) after the divergence of the cnidarians from the common ancestor that gave rise to bilaterian animals (ecdysozoans, lophotrophozoans and deuterostomes)." [4]
[1] https://en.wikipedia.org/wiki/Eumetazoa [2] https://en.wikipedia.org/wiki/Planulozoa [3] http://biologicalexceptions.blogspot.com/2015/02/mirroring-e... [4] https://www.sciencedirect.com/science/article/pii/S096098220... [5] https://pdfs.semanticscholar.org/3003/cc4844fe878fbe00167da6... - list of gene adaptations by LCA.
I read a line like that and I can't help but think of a Prometheus-style situation with the Earth and its species.
(paraphrasing Louis CK).
Most of the time, life is just maintaining the status-quo, until outside factors tilt fitness in one direction and the system readjusts.
Curious to know how this is known as a fact?
Also, I realize that in the fossil record we see "jumps" from one species to another in a relatively short time but is that how the underlying changes in DNA actually occurs? If so, how? Everything I've learned suggests that DNA modifications are made under some stochastic process.
"The researchers found 6,331 genes that were present in the common ancestor of all living animals."
"But 1,189 of the genes in the ancestral animal can’t be found in our closest known single-celled relatives."
So, 5142 genes are common between eukaryotes and prokaryotes, okay. But where is this 55% number coming from? This article is confusing.
POP, even POP3, is from the 1980s. And I'd actually newer than a lot of the stuff the internet rests on.
Ideas, bad or otherwise, from the 1990s, aren't comparatively new,.as much as “the 90s” seems to often be used as a generic term for ancient history.
So, haha, no.
This is empirical. The researchers are observing the DNA from different orders of life (based on their extant species) and comparing them. They report their quantitative similarity.
What about that is not factual?
https://www.amazon.com/Darwins-Doubt-Explosive-Origin-Intell...
https://www.forbes.com/2009/02/12/evolution-creation-proof-o...
It's also disingenuous to ask people "to have an open mind" when the overwhelming weight of scientific evidence and consensus strongly supports evolution. There needs to be a damn good reason to bother looking at a lonely contrarian argument, especially as it has likely been debunked already.
Still, I feel that couching Christian or other religious faith in "theory" language is not completely honest. I don't think anyone really supports intelligent design, as opposed to Jesus speaking the world into being design.
Even a religious theory like intelligent design or creationism should produce abundant physical evidence that could be assessed. And they should attempt to integrate with all neighboring scientific fields of study (geology, anthropology, genetics, etc). But this doesn't seem to happen.
Likewise for ID, which is a property shared between many theories which actually do make predictions. Successful predictions? Maybe not but they do count as hypotheses. (building on the point that nobody in practice actually supports ID, but instead supports a more specific genesis story that happens to fall under ID.)
Too true. A medical education is akin to parrot training; the body of knowledge a medical student must master, the manner of instruction and time frame required renders it impossible for medical students to verify their education. I have had a few scientist type friends attempt medical school, but dropped out because they rejected the lack of verification capability of everything they were being taught. Speaking to many doctors, they are afraid of their own profession. Mix in the American Medical Industry's insistence on profit, and the entire profession falls into suspicion. Doctors are blind, and their opinions need to be treated with respect towards their parrot education and the drumming out of opportunities to question their education and how that impacts a person's critical analysis capability.
Now evolution has become the popular opinion. Unsurprisingly, humans continue to be just as closed-minded as before -- unwilling to even consider or debate alternatives.
It's as if, after discovering the Earth is a sphere, continuing to entertain discussion that the Earth might be flat. It's a waste of time.