r/DeExtinctionScience

OP here: I don't think Paolini is fully aware of all of the Colossal Biosciences controversies.

Basilosaurus es un género extinto de cetáceos arqueocetos; se trata del primer cetáceo grande en aparecer en el registro fósil y es una pieza clave en el estudio de su evolución.

When I was a little kid, I remember reading about how scientists were using gene blocks to express atavistic traits. From what I remember they would block certain genes during embryogenesis (?). This would cause some genes to be expressed and others not to be. It appears if they blocked genes that evolved after a certain point, the newer genes would not be expressed. For example, if a gene that evolved 100,000 years ago is blocked, the ones that evolved since then weren't supposed to be expressed. Some genes that evolve seem to actually cause a genome to be "rearranged." Blocking them might actually cause the genome to "revert" to the earlier configuration and express atavistic genes.

This would appear to be extremely beneficial for de-extinction. We could use it by sequencing extinct animals. We would then sequence other still living animals that are genetically similar. We would then block the gene in the still living animal that evolved right after their LUCA. This would be the proto-animal. We would grow it and sequence it. Then we would see which gene evolved in the extinct animal right after the LUCA. We would change the proto-animal to have this gene. We would keep doing this until we have the same animal that went extinct. It would not be similar, it would be the same.

I think de-extinction is possibly a lot easier than we realize. If there's anyone working on it, please contact me so we could possibly set up a protocol and see if this could work.

Here's an article sent to me by u/nodnarb51 about something similar. It looks liek they used gene blocks to get the talpid phenotype expressed in chickens. Atavisms in the avian hindlimb and early developmental polarity of the limb - PMC

LUCA- Last Universal Common Ancestor

https://pmc.ncbi.nlm.nih.gov/articles/PMC8373999/

A short, excellent paper that breaks down some of the problems and issues with Colossal Biosciences' attempts at "dire wolf" cloning that were not revealed to the public: https://www.sciencedirect.com/science/article/pii/S2213671125001092

Full citation: Ilic, Dusko. "Engineered proxies and the illusion of de-extinction". Stem Cell Reports, Volume 20, Issue 6, 10 June 2025.

Key excerpt (same issues as the bucardo cloning project from 2003/2013-2014; see thread here):

> Colossal's "dire wolf" project does not represent the culmination of stem cell-based developmental and/or conservation biology (Stanton et al., 2018), as originally claimed, but rather reflects a more traditional cloning approach with synthetic augmentation. While the company has not released peer-reviewed data, publicly available sources indicate that somatic blood cells were genetically edited at approximately twenty loci and then used in somatic cell nuclear transfer (SCNT) (Max, 2025). > > These nuclei were inserted into enucleated dog oocytes, and the resulting embryos were gestated in large domestic dogs, not wolves (Figure 1). The yield was low: 2 live births from 45 embryos, reflecting persistent challenges in ex vivo developmental biology and post-edit viability. This method, reminiscent of the technique used in Dolly the sheep, bypasses pluripotency induction or in vitro gametogenesis entirely. > > Figure 1. Cloning strategy used to generate dire wolf-like canids. Somatic cells from a gray wolf were genetically engineered at approximately twenty loci using multiplex CRISPR editing to introduce traits inferred from the extinct dire wolf genome. The edited nuclei were transferred into enucleated oocytes from domestic dogs via somatic cell nuclear transfer (SCNT). The resulting embryos were implanted into surrogate dog mothers and developed into live pups exhibiting selected phenotypic traits (e.g., cranial robustness, body mass, and pigmentation) consistent with dire wolf morphology. The outcome represents phenotypic approximation, rather than genomic or ecological resurrection. > > This distinction is significant. The omission of induced pluripotent stem cell derivation or artificial gamete generation narrows the scope of technological novelty while raising well-documented concerns about the health and viability of cloned animals. SCNT-derived mammals frequently suffer from epigenetic abnormalities, metabolic disorders, and shortened lifespans. The health of Colossal’s dire wolf-like offspring has not been independently assessed or disclosed in detail. Without such data—ideally in a peer-reviewed format—it is impossible to determine whether the engineered animals are viable, fertile, or behaviorally analogous to their extinct analogs. > > The technical, ethical, and biological complexities of cloning as a de-extinction tool are not merely theoretical. A striking case is that of the bucardo (Capra pyrenaica pyrenaica), a subspecies of Spanish ibex that was declared extinct in 2000. After the death of the last known individual, scientists attempted to clone the animal using nuclei from preserved tissue and goat oocytes. In 2003, 57 embryos were implanted. Only one resulted in a live birth, and the cloned bucardo survived for less than 10 minutes due to a fatal lung defect. This event marked the first and only time a species has been brought back from extinction, only to go extinct again. The bucardo's brief return highlights the biological limitations, raising unresolved ethical questions about animal welfare, viability, and purpose of "de-extinction". > > Despite its symbolic appeal, SCNT remains a technically fragile and inefficient method for species restoration. The bucardo's brief reappearance is not an exception but a representative case. Across mammalian species, SCNT consistently exhibits low efficiency, with most attempts resulting in embryonic failure, pregnancy loss, or postnatal abnormalities. This lack of transparency underlines a critical need: any claim of functional de-extinction must be accompanied by rigorous, open peer evaluation of the methods used, the phenotypic expression achieved, and the physiological integrity of the resulting animals. Until then, the "dire wolves" remain closer to concept demonstrations than to viable ecological actors.

Key citation in this paper: Stanton et al., 2018. M.M. Stanton, E. Tzatzalos, M. Donne, N. Kolundzic, I. Helgason, D. Ilic. "Prospects for the Use of Induced Pluripotent Stem Cells (iPSC) in Animal Conservation and Environmental Protection". Stem Cell Reports 8 (2018), pp. 7-13.

The last bucardo, or Pyrenean ibex, died on January 6, 2000. However, prior to the death of Celia - the last individual - skin cells were collected in 1999, and preserved in liquid nitrogen. Celia was successfully cloned on July 30, 2003, marking the first-ever "de-extinction", though the clone died roughly 10 minutes later due to a lung defect. (Celia's cells were evaluated to see if they were still viable for cloning in 2013, but it's unclear what the testing results were, and were found to still be useable; however, the same technique used in 2003 by the same researchers failed.)

Scientists were able to successfully create 439 embryos from the frozen skin cells; of these, 57 were successfully implanted into goat surrogate mothers. However, only 7 resulted in viable pregnancies; and of these, only one made it to the live birth stage. In the past two decades since the last cloning attempt in 2003, cloning science has progressed by leaps and bounds, and cloning advances with horses in Argentina show the likely cause for the attempt's failure.

According to the 2026 article "Field of clones: How horse replicas came to dominate polo" by Maximiliano Fernández for Knowable Magazine, scientists and experts have discovered that certain techniques improve the odds of successfully cloning mammal species (horses, cows).

>In recent years, several advances have improved horse cloning, says Flávio Vieira Meirelles, a reproductive biotechnologist at the University of São Paulo, Brazil. These mainly involve methods for activation of the [donor] egg after inserting the nucleus, and cultivation conditions for the embryo. In addition, the efficiency with which the genes of the donated nucleus are reprogrammed — a process that is carried out by chemicals in the cytoplasm of the egg — has improved. > > Greater success, too, is achieved when the donated nuclei come from adult stem cells — which are capable of renewing themselves and transforming into various tissues within an organ — compared with nuclei from fully differentiated cells from a tissue such as skin. The differentiated cells carry more "memory" of their original function. Cells from young animals tend to respond better than those from older animals; and, of course, the reproductive capacity of the female surrogate mothers plays a role, too. Even with everything optimized, the birth rate per transferred embryo is low in large mammals, ranging from 3% to 10%. > > [...] In addition, explains Sebastián Demyda Peyrás, an equine geneticist at the University of Cordoba, Spain, "Epigenetic patterns in cloning are altered much more frequently than in natural pregnancies. Both factors — mitochondrial replacement and epigenetics — influence the higher rate of miscarriages and the number of clones born with health problems, placental abnormalities, or severe physical problems." (Epigenetics refers to the way that genes may be turned on or off due to the addition or removal of small chemical groups, without affecting the DNA.)

Celia, the last bucardo, died at 13 years old when a tree fell on her in Ordesa National Park in Spain, with the average bucardo lifespan being around 15-20 years old in the wild. Thus, Celia was not a young animal, which makes cloning her a more difficult task for scientists. Another factor may be the use of domesticated goat or hybrid Spanish ibex-goat oocytes, or donor eggs, for cloning the bucardo. Colossal Biosciences appears to be trying to avoid the problems that plagued the bucardo cloning project with the bluebuck by using donor eggs from the roan antelope, a closely-related species, and possibly the sable antelope.

The one clone that made it to the birth stage had abnormalities consistent with testing:

>At first, the [horse cloning] results were not encouraging. The first clones by biotechnologist Gabriel Vichera's company, Kheiron Biotech, between 2012 and 2016, were made from adult skin cells, and almost half of the foals from the 38 live births had abnormalities of the umbilical cord or placenta, or limbs that were abnormally bent. The turning point came when the company started working with stem cells from bone marrow. "This technology changed everything. Today, almost 100 percent of births are as healthy as those obtained through natural breeding," says Vichera. To date, Kheiron Biotech reports having produced a thousand cloned horses.

So, how can the chances of successfully cloning a living bucardo be improved? The first step would be to convert frozen skin cells - if still viable in 2026 - into stem cells. In 2007, scientists were able to convert adult human skin cells into pluripotent stem cells (iPSCs) by introducing four specific genes (transcription factors, called "Yamanaka factors", after scientist Dr. Shinya Yamanaka), causing them to behave like embryonic stem cells. In theory, this should improve cloning odds, especially since research indicates these factors can partially reprogram adult cells, reverting them to a younger, more functional state in a process called "cellular rejuvenation".

While re-cloning the bucardo is possible - or even plausible, with improved technology - one of the biggest issues is funding. However, if a major company like Colossal Biosciences chooses to take up cloning the bucardo, it could serve as an important "stepping stone" towards Colossal's ultimate goal of cloning the bluebuck. This is because, much like with the bucardo, the DNA sample that Colossal is working with came from skin cells scraped from the ear of a 200-year-old male specimen from a Swedish museum - and, if Colossal wants to use DNA from more than one specimen, they'll have to rely on skin samples from other museum specimens.

"It is not technology bound. It is money bound," said Ben Novak, the lead scientist for Revive & Restore's passenger pigeon program. "If I had a rich oligarch that gave us $25 million in funding right now, I'd guarantee we'd have a passenger pigeon in five years."

Indeed, Colossal may be working with, or copying, Kheiron Biotech and their techniques, as the company announced that their scientific team achieved breakthroughs in generating the first-ever roan antelope induced pluripotent stem cells (iPSCs) and successful ovum pickup (OPU) techniques, enabling genome editing to introduce bluebuck traits. [Kheiron Biotech developed use of a technique called "transvaginal aspiration" for collecting oocytes from live females, which resulted in better success rates for "ovum pickup" (OPU).]

Quote: "With oocytes obtained using transvaginal aspiration, the proportion of embryos that reach the blastocyst stage is around 35%, compared to just 26% in oocytes obtained from slaughterhouses. The difference widens in later stages: Among mares that remain pregnant after day 42, just over half (50%) of pregnancies derived from eggs obtained by transvaginal aspiration result in healthy foals, [vs. just 10% for non-live donors]."

I would recommend that scientists partner with Kheiron Biotech in Argentina to re-clone the bucardo. In December 2024, the company announced the birth of five foals that had been genetically edited using the CRISPR-Cas9 technique, a major global milestone. Vichera presented the achievement as proof of concept and a preview of a scenario in which it will be possible not only to clone animals, but also to introduce specific modifications to their genomes. Thus, Kheiron Biotech's findings would be highly useful for "de-extinction".

A caveat emptor: "Despite the technical advances, significant losses occur at each stage. It is estimated that, out of every 100 embryos, 20 reach the blastocyst stage and are transferred. Of these, 10 are successfully implanted in surrogate mares, and of those 10, only five reach full term. Even among foals born, there can be problems with health and development, although the lack of public data prevents this from being quantified accurately. The high loss rate partly explains the high cost of the procedure. Although the price has fallen in recent years thanks to technical advances, cloning a horse...[still] costs around $40,000."

Fantastic paper that basically lays out the Colossal Biosciences playbook: https://law.stanford.edu/wp-content/uploads/2018/05/carlin.pdf

Full citation: Norman F. Carlin, Ilan Wurman, and Tamara Zakim. "How to Permit Your Mammoth: Some Legal Implications of 'De-Extinction'". vol 33 Stanford Environmental Law Journal 3 (2014).

Most notably, the paper indicates why Colossal Biosciences has been courting Trump administration officials - particularly within the Food & Drug Administration (FDA) and U.S. Department of Agriculture (USDA) - and pushing for "deregulation", with the company likely seeing additional restrictions, regulations, and laws that apply to GMOs (genetically modified organisms) - what the FDA has more lately been specifying to include "Intentional Genomic Alterations" (IGAs) - as "red tape" that hinders both "de-extinction" and "scientific progress". However, whereas this paper points out that Colossal could try to get their "dire wolves" listed as an "endangered species" under the Endangered Species Act (ESA), some Republican politicians are seeking to gut the ESA through legislation.

It's also highly likely that Colossal Biosciences, which is now worth over $10 billion, has already retained or hired a legal team to argue their case in court, as well as to lobby politicians to introduce, vote for, and pass new legislation that favors Colossal's goals. However, due to a "deep split" among environmental and conservation groups as to whether GMOs should be released into the wild - even for "conservation purposes" (ex. "de-extinction") - it is also highly likely that Colossal will face litigation from one or more of these groups at some point. This would mean potentially spending millions on lawyers and legal fees through litigating cases for years, or even decades, which would draw even more funds away from conservation efforts to support "de-extinction" instead.

Could this mean "more attention drawn to environmentalism and conservation efforts", as Colossal Biosciences CEO Ben Lamm claims? Yes, but not in the way Lamm probably hoped. Instead, the current forecast indicates a years-long legal and political battle ahead for Colossal both in the United States and on an international scale, especially as Lamm seeks to bring "de-extinction" to the mainstream in an effort to raise public support; court wealthy investors; appeal to the news media; and more. Thus far, Colossal has failed to impress most scientists and experts, who have expressed wariness of the company due to secrecy; lack of transparency; refusal to share scientific research; etc.